From tpais@domain.hid Wed Apr 06 17:39:27 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7UpE-0007lO-5e for relax-users@domain.hid; Wed, 06 Apr 2011 17:39:27 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=0.5 required=3.3 tests=BAYES_40,HTML_MESSAGE autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail4.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7UpD-0007lF-RV for relax-users@domain.hid; Wed, 06 Apr 2011 17:39:20 +0200 Received: from mail4.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail4.itqb.unl.pt (Postfix) with ESMTP id AE6049480F4 for ; Wed, 6 Apr 2011 16:39:17 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail4.itqb.unl.pt (Postfix) with ESMTP id 901C59480E4 for ; Wed, 6 Apr 2011 16:39:17 +0100 (WEST) From: "Tiago Pais" To: Subject: How to set S2f to 0.111? Date: Wed, 6 Apr 2011 16:39:18 +0100 Message-ID: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0051_01CBF479.2CA3BEE0" X-Mailer: Microsoft Office Outlook 11 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 Thread-Index: Acv0cMqqdpfu+M5iRJ65XAQo+eABTg== X-Virus-Scanned: ClamAV using ClamSMTP X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Apr 2011 15:39:27 -0000 This is a multi-part message in MIME format. ------=_NextPart_000_0051_01CBF479.2CA3BEE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I would like to make an analysis of side-chain relaxation data with the = S2f parameter (in model 5) set to 0.111. Is it possible to do this with RELAX? How? Thanks in advance. Cheers Tiago P =20 ************************************** Tiago Pais, PhD. student Cell Physiology & NMR Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras =20 ------=_NextPart_000_0051_01CBF479.2CA3BEE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

I would like to make an analysis of side-chain = relaxation data with the S2f parameter (in model 5) set to = 0.111.

Is it possible to do this with RELAX? = How?

Thanks in advance.

Cheers

Tiago P

 

**************************************

Tiago Pais, PhD. student

Cell Physiology & NMR

Instituto de Tecnologia Qu=EDmica e = Biol=F3gica-Oeiras

 



__________ Information from ESET NOD32 Antivirus, version of = virus signature database 6019 (20110406) __________

The message = was checked by ESET NOD32 Antivirus.

http://www.eset.com
------=_NextPart_000_0051_01CBF479.2CA3BEE0-- From edward.dauvergne@domain.hid Wed Apr 06 18:13:58 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7VMd-0003GI-1J for relax-users@domain.hid; Wed, 06 Apr 2011 18:13:58 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-3.6 required=3.3 tests=BAYES_00,RCVD_IN_DNSWL_LOW autolearn=ham version=3.2.5 Received: from mail-vw0-f51.google.com ([209.85.212.51]) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7VMc-0003Eg-Tp for relax-users@domain.hid; Wed, 06 Apr 2011 18:13:51 +0200 Received: by vws20 with SMTP id 20so1184750vws.10 for ; Wed, 06 Apr 2011 09:13:29 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:in-reply-to:references:date :message-id:subject:from:to:cc:content-type :content-transfer-encoding; bh=lsXDWihQysaz8nBIKLinikzNG8JzHNBAkkPRsbJMtw0=; b=mR9m/PvWgk90Msp6/LEjmSVf2OEES6j0s5iCLZaMOo8I7jCXflYeKPtfbS+U6XSNun Y6vT3dg9Oxf2uZ8+DlgJsBalzN4wJ5FiJ7jIi1JnLyUMDYuoxRD1Rd5oip+drObEyT2H jcCdSmA8BlLeDKpdd47UriiPey3U97dYdi4Rs= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :cc:content-type:content-transfer-encoding; b=gGXguWVN7ruK/sqtB8pIYyYIoiuRHSoOQv0eyV0b7BqJjhwDo1J0NBY/rvodsIDBlN XXmLb9PXlTUHJSR/OYTjYf1Qn2EoRLWzM2j0eh+tKeRMAmhUGqHZGQcDJWY+BCTMD3EP MwgZ8IkvVgmgOaLiFGCEhN/OX9cMbskaF5cpw= MIME-Version: 1.0 Received: by 10.52.100.1 with SMTP id eu1mr1651834vdb.174.1302106409130; Wed, 06 Apr 2011 09:13:29 -0700 (PDT) Received: by 10.52.164.101 with HTTP; Wed, 6 Apr 2011 09:13:29 -0700 (PDT) In-Reply-To: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> Date: Wed, 6 Apr 2011 18:13:29 +0200 Message-ID: Subject: Re: How to set S2f to 0.111? From: "Edward d'Auvergne" To: Tiago Pais Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Apr 2011 16:13:58 -0000 Hi, Unfortunately, there is no ability to fix one of the model-free parameters during optimisation in relax yet. This is something that has been requested one or two times over the years. This is complicated as the gradients and Hessians (first and second partial derivates) need to be modified with this in mind, as the curvature of the space changes. The fixed parameter is not part of the gradient or Hessian, and has to be removed. This really complicates the target function, gradient, and Hessian and, due to the low demand, has not been implemented. Are you able to optimise this parameter and see if you get 0.111? And are you able to extract the timescale of this process (the methyl group rotamer jumps)? From memory, someone has optimsed these models using a grid search. This coarse optimisation can be performed in relax as you are able to specify the fine details of the grid search. It is slower, but will do the job. You could even implement a zooming grid search if your scripting skills are up to it to be able to relatively quickly find the parameters to high precision. Anyway, I hope this info helps. Regards, Edward On 6 April 2011 17:39, Tiago Pais wrote: > Hi, > > I would like to make an analysis of side-chain relaxation data with the S= 2f > parameter (in model 5) set to 0.111. > > Is it possible to do this with RELAX? How? > > Thanks in advance. > > Cheers > > Tiago P > > > > ************************************** > > Tiago Pais, PhD. student > > Cell Physiology & NMR > > Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras > > > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > relax-users@domain.hid > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-users > > From tpais@domain.hid Wed Apr 06 18:38:53 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7Vkk-000634-5G for relax-users@domain.hid; Wed, 06 Apr 2011 18:38:53 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail4.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7Vkj-000630-PJ for relax-users@domain.hid; Wed, 06 Apr 2011 18:38:46 +0200 Received: from mail4.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail4.itqb.unl.pt (Postfix) with ESMTP id 170049480F4; Wed, 6 Apr 2011 17:38:45 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail4.itqb.unl.pt (Postfix) with ESMTP id 09DD79480DC; Wed, 6 Apr 2011 17:38:45 +0100 (WEST) From: "Tiago Pais" To: "'Edward d'Auvergne'" References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> Subject: RE: How to set S2f to 0.111? Date: Wed, 6 Apr 2011 17:38:46 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Mailer: Microsoft Office Outlook 11 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 In-Reply-To: Thread-Index: Acv0dZGFjhPMXDJeT9SmNz6Hr1/TfgAAnaHA X-Virus-Scanned: ClamAV using ClamSMTP Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Apr 2011 16:38:53 -0000 Hi Ed, Thanks for the quick reply. Let's see if I understand your suggestion. For example, the = mf_multimodel.py sample script performs a grid search minimization using the grid_search function. So if I insert an array of upper and lower bounds for the parameters in the model I can constrain the interval of possible = results, correct? If so, what is the sequence for the parameters in the array? TP -----Original Message----- From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid Sent: quarta-feira, 6 de Abril de 2011 17:13 To: Tiago Pais Cc: relax-users@domain.hid Subject: Re: How to set S2f to 0.111? Hi, Unfortunately, there is no ability to fix one of the model-free parameters during optimisation in relax yet. This is something that has been requested one or two times over the years. This is complicated as the gradients and Hessians (first and second partial derivates) need to be modified with this in mind, as the curvature of the space changes. The fixed parameter is not part of the gradient or Hessian, and has to be removed. This really complicates the target function, gradient, and Hessian and, due to the low demand, has not been implemented. Are you able to optimise this parameter and see if you get 0.111? And are you able to extract the timescale of this process (the methyl group rotamer jumps)? From memory, someone has optimsed these models using a grid search. This coarse optimisation can be performed in relax as you are able to specify the fine details of the grid search. It is slower, but will do the job. You could even implement a zooming grid search if your scripting skills are up to it to be able to relatively quickly find the parameters to high precision. Anyway, I hope this info helps. Regards, Edward On 6 April 2011 17:39, Tiago Pais wrote: > Hi, > > I would like to make an analysis of side-chain relaxation data with = the S2f > parameter (in model 5) set to 0.111. > > Is it possible to do this with RELAX? How? > > Thanks in advance. > > Cheers > > Tiago P > > > > ************************************** > > Tiago Pais, PhD. student > > Cell Physiology & NMR > > Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > relax-users@domain.hid > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-users > > __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From edward.dauvergne@domain.hid Wed Apr 06 18:42:47 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7VoU-0006qo-UF for relax-users@domain.hid; Wed, 06 Apr 2011 18:42:47 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from mail-vx0-f179.google.com ([209.85.220.179]) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7VoU-0006qK-QA for relax-users@domain.hid; Wed, 06 Apr 2011 18:42:38 +0200 Received: by vxi40 with SMTP id 40so1226600vxi.10 for ; Wed, 06 Apr 2011 09:42:16 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; bh=HdtTI6KripsW16JhXMdHG0GEoU1N5uiLdMyibTWGsFE=; b=dmhqDLi8QBLZCAstfoHuIyJ/wDjz8GaKRYof0SZpqny8sy1jZb+WEcGsZAInyIfmXF Vcn1cZbzqZNULiF4oz0ruZRxoESsv/5C5Os5tEymCuwBLo2ocTwLx9MKMycJ0eq/LJAs OW0/I2/esv8Fx928xLnCQaawp5qWUyvN+1quM= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; b=frvPNwu2YUxEqG04Tillrb1kUVh5lyENK5SN7YqcM+HNUs25w5u2pmOc8yyRtLbhKT OP3u3OwMlsYkefPecF7AljWl+hLmiwbsi++MrF+Z9yRc4yjQxTHpe/+wT9mFWj0EWrB2 7x6R4ec6+8Dph25MEprsq2RgBZhL7mq2MxkRA= MIME-Version: 1.0 Received: by 10.52.92.38 with SMTP id cj6mr1612001vdb.254.1302108135875; Wed, 06 Apr 2011 09:42:15 -0700 (PDT) Sender: edward.dauvergne@domain.hid Received: by 10.52.164.101 with HTTP; Wed, 6 Apr 2011 09:42:15 -0700 (PDT) In-Reply-To: References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> Date: Wed, 6 Apr 2011 18:42:15 +0200 X-Google-Sender-Auth: XwfsNEabK2ULQaXUqnmWm-cPDWA Message-ID: Subject: Re: How to set S2f to 0.111? From: "Edward d'Auvergne" To: Tiago Pais Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Apr 2011 16:42:47 -0000 Hi, That is roughly correct. Just set the lower and upper bound to 0.111 and set the number of increments for that parameter to 1. Then it is like a grid search without S2f being present, or being fixed to 0.111. Regards, Edward On 6 April 2011 18:38, Tiago Pais wrote: > Hi Ed, > Thanks for the quick reply. > Let's see if I understand your suggestion. For example, the mf_multimodel= .py > sample script performs a grid search minimization using the grid_search > function. So if I insert an array of upper and lower bounds for the > parameters in the model I can constrain the interval of possible results, > correct? If so, what is the sequence for the parameters in the array? > TP > > > > -----Original Message----- > From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] > Sent: quarta-feira, 6 de Abril de 2011 17:13 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > Unfortunately, there is no ability to fix one of the model-free > parameters during optimisation in relax yet. =A0This is something that > has been requested one or two times over the years. =A0This is > complicated as the gradients and Hessians (first and second partial > derivates) need to be modified with this in mind, as the curvature of > the space changes. =A0The fixed parameter is not part of the gradient or > Hessian, and has to be removed. =A0This really complicates the target > function, gradient, and Hessian and, due to the low demand, has not > been implemented. > > Are you able to optimise this parameter and see if you get 0.111? =A0And > are you able to extract the timescale of this process (the methyl > group rotamer jumps)? =A0From memory, someone has optimsed these models > using a grid search. =A0This coarse optimisation can be performed in > relax as you are able to specify the fine details of the grid search. > It is slower, but will do the job. =A0You could even implement a zooming > grid search if your scripting skills are up to it to be able to > relatively quickly find the parameters to high precision. =A0Anyway, I > hope this info helps. > > Regards, > > Edward > > > > > > On 6 April 2011 17:39, Tiago Pais wrote: >> Hi, >> >> I would like to make an analysis of side-chain relaxation data with the > S2f >> parameter (in model 5) set to 0.111. >> >> Is it possible to do this with RELAX? How? >> >> Thanks in advance. >> >> Cheers >> >> Tiago P >> >> >> >> ************************************** >> >> Tiago Pais, PhD. student >> >> Cell Physiology & NMR >> >> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users mailing list >> relax-users@domain.hid >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-users >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > From tpais@domain.hid Wed Apr 06 18:54:36 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7Vzx-0007Pq-AZ for relax-users@domain.hid; Wed, 06 Apr 2011 18:54:36 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail4.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7Vzx-0007Pj-3n for relax-users@domain.hid; Wed, 06 Apr 2011 18:54:29 +0200 Received: from mail4.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail4.itqb.unl.pt (Postfix) with ESMTP id 25F609480ED; Wed, 6 Apr 2011 17:54:28 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail4.itqb.unl.pt (Postfix) with ESMTP id 191089480EC; Wed, 6 Apr 2011 17:54:28 +0100 (WEST) From: "Tiago Pais" To: "'Edward d'Auvergne'" References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> Subject: RE: How to set S2f to 0.111? Date: Wed, 6 Apr 2011 17:54:29 +0100 Message-ID: <78F8FACF15244E5DB30D23776CF896D8@domain.hid> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Mailer: Microsoft Office Outlook 11 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 In-Reply-To: Thread-Index: Acv0eZd9ec9Ib1UHQKOfN/a57j3gDAAATfug X-Virus-Scanned: ClamAV using ClamSMTP Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Apr 2011 16:54:36 -0000 Ok, Im sorry to insist but I am probably missing something here. How do I = state which bound goes with which parameter? That is, which position in the = array bound corresponds to the S2f parameter? Regards. TP -----Original Message----- From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 6 de Abril de 2011 17:42 To: Tiago Pais Cc: relax-users@domain.hid Subject: Re: How to set S2f to 0.111? Hi, That is roughly correct. Just set the lower and upper bound to 0.111 and set the number of increments for that parameter to 1. Then it is like a grid search without S2f being present, or being fixed to 0.111. Regards, Edward On 6 April 2011 18:38, Tiago Pais wrote: > Hi Ed, > Thanks for the quick reply. > Let's see if I understand your suggestion. For example, the mf_multimodel.py > sample script performs a grid search minimization using the = grid_search > function. So if I insert an array of upper and lower bounds for the > parameters in the model I can constrain the interval of possible = results, > correct? If so, what is the sequence for the parameters in the array? > TP > > > > -----Original Message----- > From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] > Sent: quarta-feira, 6 de Abril de 2011 17:13 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > Unfortunately, there is no ability to fix one of the model-free > parameters during optimisation in relax yet. =A0This is something that > has been requested one or two times over the years. =A0This is > complicated as the gradients and Hessians (first and second partial > derivates) need to be modified with this in mind, as the curvature of > the space changes. =A0The fixed parameter is not part of the gradient = or > Hessian, and has to be removed. =A0This really complicates the target > function, gradient, and Hessian and, due to the low demand, has not > been implemented. > > Are you able to optimise this parameter and see if you get 0.111? = =A0And > are you able to extract the timescale of this process (the methyl > group rotamer jumps)? =A0From memory, someone has optimsed these = models > using a grid search. =A0This coarse optimisation can be performed in > relax as you are able to specify the fine details of the grid search. > It is slower, but will do the job. =A0You could even implement a = zooming > grid search if your scripting skills are up to it to be able to > relatively quickly find the parameters to high precision. =A0Anyway, I > hope this info helps. > > Regards, > > Edward > > > > > > On 6 April 2011 17:39, Tiago Pais wrote: >> Hi, >> >> I would like to make an analysis of side-chain relaxation data with = the > S2f >> parameter (in model 5) set to 0.111. >> >> Is it possible to do this with RELAX? How? >> >> Thanks in advance. >> >> Cheers >> >> Tiago P >> >> >> >> ************************************** >> >> Tiago Pais, PhD. student >> >> Cell Physiology & NMR >> >> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users mailing list >> relax-users@domain.hid >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-users >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From edward.dauvergne@domain.hid Wed Apr 06 19:05:11 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7WAB-0000wa-29 for relax-users@domain.hid; Wed, 06 Apr 2011 19:05:11 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from mail-vx0-f179.google.com ([209.85.220.179]) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7WAA-0000uN-R8 for relax-users@domain.hid; Wed, 06 Apr 2011 19:05:03 +0200 Received: by vxi40 with SMTP id 40so1245205vxi.10 for ; Wed, 06 Apr 2011 10:04:40 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; bh=vUHJ0p/zOP/fdV0Nbq/1Mz25VgjzdXg942CSMraATwQ=; b=oCOHpiw55yxVpJXrKVoLWOYNxVs+mlU6xyIs8aklWT8sFfZMgmlRu9ySaj0IL4w3Ub Soey1uW3L3FVWqrnGyZz9R2Z05QpOoMG9SsOzUKJ9UsHxe7n+HkEW+8PoYqkkH+kSYCA GfhoHdn2Gb2NIfTL333bufM09EggVVh2D5PF4= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; b=TvZEld4jb9pQR4RzsiVStaVJDib1ZYwgg2jzhF/OXCkXb/a/vapM0xjjKCs/gpV9uA YM6V3xvZo9sbWOvUhkgk7gh1hW6VUXeD42a0D+/+Qo3lTQv9npmdGommsxPo8Lrfwevh QwjuFnDaAINJQnyGOcwNJiZ5ErQXTAdsDY81E= MIME-Version: 1.0 Received: by 10.52.73.130 with SMTP id l2mr520985vdv.14.1302109480734; Wed, 06 Apr 2011 10:04:40 -0700 (PDT) Sender: edward.dauvergne@domain.hid Received: by 10.52.164.101 with HTTP; Wed, 6 Apr 2011 10:04:40 -0700 (PDT) In-Reply-To: <78F8FACF15244E5DB30D23776CF896D8@domain.hid> References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> <78F8FACF15244E5DB30D23776CF896D8@domain.hid> Date: Wed, 6 Apr 2011 19:04:40 +0200 X-Google-Sender-Auth: boaZ9pa1Ot7Rl3JAoVVMB192JqE Message-ID: Subject: Re: How to set S2f to 0.111? From: "Edward d'Auvergne" To: Tiago Pais Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Apr 2011 17:05:11 -0000 Hi, These match the parameters as listed in the help for the model_free.select_model() user function. The grid search arrays match the parameter arrays. Regards, Edward On 6 April 2011 18:54, Tiago Pais wrote: > Ok, > Im sorry to insist but I am probably missing something here. How do I sta= te > which bound goes with which parameter? That is, which position in the arr= ay > bound corresponds to the S2f parameter? > Regards. > TP > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Abril de 2011 17:42 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > That is roughly correct. =A0Just set the lower and upper bound to 0.111 > and set the number of increments for that parameter to 1. =A0Then it is > like a grid search without S2f being present, or being fixed to 0.111. > > Regards, > > Edward > > > > On 6 April 2011 18:38, Tiago Pais wrote: >> Hi Ed, >> Thanks for the quick reply. >> Let's see if I understand your suggestion. For example, the > mf_multimodel.py >> sample script performs a grid search minimization using the grid_search >> function. So if I insert an array of upper and lower bounds for the >> parameters in the model I can constrain the interval of possible results= , >> correct? If so, what is the sequence for the parameters in the array? >> TP >> >> >> >> -----Original Message----- >> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >> Sent: quarta-feira, 6 de Abril de 2011 17:13 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> Unfortunately, there is no ability to fix one of the model-free >> parameters during optimisation in relax yet. =A0This is something that >> has been requested one or two times over the years. =A0This is >> complicated as the gradients and Hessians (first and second partial >> derivates) need to be modified with this in mind, as the curvature of >> the space changes. =A0The fixed parameter is not part of the gradient or >> Hessian, and has to be removed. =A0This really complicates the target >> function, gradient, and Hessian and, due to the low demand, has not >> been implemented. >> >> Are you able to optimise this parameter and see if you get 0.111? =A0And >> are you able to extract the timescale of this process (the methyl >> group rotamer jumps)? =A0From memory, someone has optimsed these models >> using a grid search. =A0This coarse optimisation can be performed in >> relax as you are able to specify the fine details of the grid search. >> It is slower, but will do the job. =A0You could even implement a zooming >> grid search if your scripting skills are up to it to be able to >> relatively quickly find the parameters to high precision. =A0Anyway, I >> hope this info helps. >> >> Regards, >> >> Edward >> >> >> >> >> >> On 6 April 2011 17:39, Tiago Pais wrote: >>> Hi, >>> >>> I would like to make an analysis of side-chain relaxation data with the >> S2f >>> parameter (in model 5) set to 0.111. >>> >>> Is it possible to do this with RELAX? How? >>> >>> Thanks in advance. >>> >>> Cheers >>> >>> Tiago P >>> >>> >>> >>> ************************************** >>> >>> Tiago Pais, PhD. student >>> >>> Cell Physiology & NMR >>> >>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users mailing list >>> relax-users@domain.hid >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-users >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > From tpais@domain.hid Wed Apr 06 19:08:29 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7WDO-0001N8-59 for relax-users@domain.hid; Wed, 06 Apr 2011 19:08:29 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail4.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7WDN-0001N2-Vm for relax-users@domain.hid; Wed, 06 Apr 2011 19:08:22 +0200 Received: from mail4.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail4.itqb.unl.pt (Postfix) with ESMTP id A496E9480EE; Wed, 6 Apr 2011 18:08:21 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail4.itqb.unl.pt (Postfix) with ESMTP id 825C49480EC; Wed, 6 Apr 2011 18:08:21 +0100 (WEST) From: "Tiago Pais" To: "'Edward d'Auvergne'" References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid><78F8FACF15244E5DB30D23776CF896D8@domain.hid> Subject: RE: How to set S2f to 0.111? Date: Wed, 6 Apr 2011 18:08:22 +0100 Message-ID: <22E69BAF08AC4AD9A74DEFB1C1AFCBEE@Mercurio> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Mailer: Microsoft Office Outlook 11 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 In-Reply-To: Thread-Index: Acv0fL6JrwDamDJPSZGyu0cnlw81BQAAF62Q X-Virus-Scanned: ClamAV using ClamSMTP Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Apr 2011 17:08:29 -0000 Good!=20 I'll let you know how it worked out. Thank you. Regards Tiago -----Original Message----- From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 6 de Abril de 2011 18:05 To: Tiago Pais Cc: relax-users@domain.hid Subject: Re: How to set S2f to 0.111? Hi, These match the parameters as listed in the help for the model_free.select_model() user function. The grid search arrays match the parameter arrays. Regards, Edward On 6 April 2011 18:54, Tiago Pais wrote: > Ok, > Im sorry to insist but I am probably missing something here. How do I state > which bound goes with which parameter? That is, which position in the array > bound corresponds to the S2f parameter? > Regards. > TP > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Abril de 2011 17:42 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > That is roughly correct. =A0Just set the lower and upper bound to = 0.111 > and set the number of increments for that parameter to 1. =A0Then it = is > like a grid search without S2f being present, or being fixed to 0.111. > > Regards, > > Edward > > > > On 6 April 2011 18:38, Tiago Pais wrote: >> Hi Ed, >> Thanks for the quick reply. >> Let's see if I understand your suggestion. For example, the > mf_multimodel.py >> sample script performs a grid search minimization using the = grid_search >> function. So if I insert an array of upper and lower bounds for the >> parameters in the model I can constrain the interval of possible = results, >> correct? If so, what is the sequence for the parameters in the array? >> TP >> >> >> >> -----Original Message----- >> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >> Sent: quarta-feira, 6 de Abril de 2011 17:13 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> Unfortunately, there is no ability to fix one of the model-free >> parameters during optimisation in relax yet. =A0This is something = that >> has been requested one or two times over the years. =A0This is >> complicated as the gradients and Hessians (first and second partial >> derivates) need to be modified with this in mind, as the curvature of >> the space changes. =A0The fixed parameter is not part of the gradient = or >> Hessian, and has to be removed. =A0This really complicates the target >> function, gradient, and Hessian and, due to the low demand, has not >> been implemented. >> >> Are you able to optimise this parameter and see if you get 0.111? = =A0And >> are you able to extract the timescale of this process (the methyl >> group rotamer jumps)? =A0From memory, someone has optimsed these = models >> using a grid search. =A0This coarse optimisation can be performed in >> relax as you are able to specify the fine details of the grid search. >> It is slower, but will do the job. =A0You could even implement a = zooming >> grid search if your scripting skills are up to it to be able to >> relatively quickly find the parameters to high precision. =A0Anyway, = I >> hope this info helps. >> >> Regards, >> >> Edward >> >> >> >> >> >> On 6 April 2011 17:39, Tiago Pais wrote: >>> Hi, >>> >>> I would like to make an analysis of side-chain relaxation data with = the >> S2f >>> parameter (in model 5) set to 0.111. >>> >>> Is it possible to do this with RELAX? How? >>> >>> Thanks in advance. >>> >>> Cheers >>> >>> Tiago P >>> >>> >>> >>> ************************************** >>> >>> Tiago Pais, PhD. student >>> >>> Cell Physiology & NMR >>> >>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users mailing list >>> relax-users@domain.hid >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-users >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From tpais@domain.hid Wed Apr 06 19:51:59 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7WtU-0005dy-MF for relax-users@domain.hid; Wed, 06 Apr 2011 19:51:59 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail4.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7WtU-0005du-Av for relax-users@domain.hid; Wed, 06 Apr 2011 19:51:52 +0200 Received: from mail4.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail4.itqb.unl.pt (Postfix) with ESMTP id E8F589480AA; Wed, 6 Apr 2011 18:51:51 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail4.itqb.unl.pt (Postfix) with ESMTP id CE4B09480A8; Wed, 6 Apr 2011 18:51:51 +0100 (WEST) From: "Tiago Pais" To: "'Edward d'Auvergne'" References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid><78F8FACF15244E5DB30D23776CF896D8@domain.hid> Subject: RE: How to set S2f to 0.111? Date: Wed, 6 Apr 2011 18:51:52 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Mailer: Microsoft Office Outlook 11 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 In-Reply-To: Thread-Index: Acv0fL6JrwDamDJPSZGyu0cnlw81BQABhKoA X-Virus-Scanned: ClamAV using ClamSMTP Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 06 Apr 2011 17:51:59 -0000 I used the expression like this: grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], inc=3D[1, = 11, 11]) But I get the following error: Unconstrained grid search size: 121 (constraints may decrease this = size). Traceback (most recent call last): File "/usr/local/bin/relax", line 418, in Relax() File "/usr/local/bin/relax", line 127, in __init__ self.interpreter.run(self.script_file) File "/usr/local/relax/prompt/interpreter.py", line 276, in run return run_script(intro=3Dself.__intro_string, local=3Dself.local, script_file=3Dscript_file, quit=3Dself.__quit_flag, show_script=3Dself.__show_script, = raise_relax_error=3Dself.__raise_relax_error) File "/usr/local/relax/prompt/interpreter.py", line 537, in run_script return console.interact(intro, local, script_file, quit, show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) File "/usr/local/relax/prompt/interpreter.py", line 433, in interact_script execfile(script_file, local) File "mf_multimodel_m5S2f0111.py", line 82, in grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], inc=3D[1, = 11, 11]) File "/usr/local/relax/prompt/minimisation.py", line 156, in = grid_search minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, constraints=3Dconstraints, verbosity=3Dverbosity) File "/usr/local/relax/generic_fns/minimise.py", line 191, in = grid_search grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, = constraints=3Dconstraints, verbosity=3Dverbosity) File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 479, in grid_search self.minimise(min_algor=3D'grid', lower=3Dlower, upper=3Dupper, = inc=3Dinc, constraints=3Dconstraints, verbosity=3Dverbosity, sim_index=3Dsim_index) File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 922, in minimise min_options =3D self.grid_search_config(num_params, spin=3Dspin, lower=3Dlower, upper=3Dupper, inc=3Dinc, = scaling_matrix=3Dscaling_matrix) File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 554, in grid_search_config self.grid_search_config_fin(min_options, lower, upper, = scaling_matrix) File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 631, in grid_search_config_fin for i in xrange(n): NameError: global name 'n' is not defined Any ideas? Cheers Tiago -----Original Message----- From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 6 de Abril de 2011 18:05 To: Tiago Pais Cc: relax-users@domain.hid Subject: Re: How to set S2f to 0.111? Hi, These match the parameters as listed in the help for the model_free.select_model() user function. The grid search arrays match the parameter arrays. Regards, Edward On 6 April 2011 18:54, Tiago Pais wrote: > Ok, > Im sorry to insist but I am probably missing something here. How do I state > which bound goes with which parameter? That is, which position in the array > bound corresponds to the S2f parameter? > Regards. > TP > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Abril de 2011 17:42 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > That is roughly correct. =A0Just set the lower and upper bound to = 0.111 > and set the number of increments for that parameter to 1. =A0Then it = is > like a grid search without S2f being present, or being fixed to 0.111. > > Regards, > > Edward > > > > On 6 April 2011 18:38, Tiago Pais wrote: >> Hi Ed, >> Thanks for the quick reply. >> Let's see if I understand your suggestion. For example, the > mf_multimodel.py >> sample script performs a grid search minimization using the = grid_search >> function. So if I insert an array of upper and lower bounds for the >> parameters in the model I can constrain the interval of possible = results, >> correct? If so, what is the sequence for the parameters in the array? >> TP >> >> >> >> -----Original Message----- >> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >> Sent: quarta-feira, 6 de Abril de 2011 17:13 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> Unfortunately, there is no ability to fix one of the model-free >> parameters during optimisation in relax yet. =A0This is something = that >> has been requested one or two times over the years. =A0This is >> complicated as the gradients and Hessians (first and second partial >> derivates) need to be modified with this in mind, as the curvature of >> the space changes. =A0The fixed parameter is not part of the gradient = or >> Hessian, and has to be removed. =A0This really complicates the target >> function, gradient, and Hessian and, due to the low demand, has not >> been implemented. >> >> Are you able to optimise this parameter and see if you get 0.111? = =A0And >> are you able to extract the timescale of this process (the methyl >> group rotamer jumps)? =A0From memory, someone has optimsed these = models >> using a grid search. =A0This coarse optimisation can be performed in >> relax as you are able to specify the fine details of the grid search. >> It is slower, but will do the job. =A0You could even implement a = zooming >> grid search if your scripting skills are up to it to be able to >> relatively quickly find the parameters to high precision. =A0Anyway, = I >> hope this info helps. >> >> Regards, >> >> Edward >> >> >> >> >> >> On 6 April 2011 17:39, Tiago Pais wrote: >>> Hi, >>> >>> I would like to make an analysis of side-chain relaxation data with = the >> S2f >>> parameter (in model 5) set to 0.111. >>> >>> Is it possible to do this with RELAX? How? >>> >>> Thanks in advance. >>> >>> Cheers >>> >>> Tiago P >>> >>> >>> >>> ************************************** >>> >>> Tiago Pais, PhD. student >>> >>> Cell Physiology & NMR >>> >>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users mailing list >>> relax-users@domain.hid >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-users >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From edward.dauvergne@domain.hid Thu Apr 07 11:46:15 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7lmx-0002AX-Pp for relax-users@domain.hid; Thu, 07 Apr 2011 11:46:15 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from mail-vx0-f179.google.com ([209.85.220.179]) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7lmx-0002AJ-IY for relax-users@domain.hid; Thu, 07 Apr 2011 11:46:07 +0200 Received: by vxi40 with SMTP id 40so1730195vxi.10 for ; Thu, 07 Apr 2011 02:45:45 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; bh=AQ4anLQ8aypA/2Cr8F+QwCN7x45In+H3kvUCylOsnE8=; b=gdyX7aJMsf9eh8q6lUDLvS3ZC+ClN0H6zNaurwzpnWvFPBt8hzEM2dxE2gB6OwocXK qkZh4IFbBpNypKXiu7++4ShtfYbJhEbbPZur+qlVhlPK/8YjTqHA3cqcarIK9b5UeaxX lK0cUaMI5JIOfeZjULcU2PqEIEBVlxVObBmo4= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; b=uWfSUvRV2FBj2vvvPI44GjQzT7gjV/FfiodhGDUfiSanJPG02ap2aDhSAG0Dgto/27 Bzti9r57jibF3BmBUCNSHCFd5Z9LBYHyZoW1Njjopv+oXNeTPWbsC3YPtaryBzu1KVLZ 6xDvfJi5F3CREKH+LjM4rckjXqq+w2rXK9yr4= MIME-Version: 1.0 Received: by 10.52.66.241 with SMTP id i17mr949849vdt.54.1302169545313; Thu, 07 Apr 2011 02:45:45 -0700 (PDT) Sender: edward.dauvergne@domain.hid Received: by 10.52.164.101 with HTTP; Thu, 7 Apr 2011 02:45:45 -0700 (PDT) In-Reply-To: References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> <78F8FACF15244E5DB30D23776CF896D8@domain.hid> Date: Thu, 7 Apr 2011 11:45:45 +0200 X-Google-Sender-Auth: 1FGAVhAen7SHkW107pOM1cTf1jI Message-ID: Subject: Re: How to set S2f to 0.111? From: "Edward d'Auvergne" To: Tiago Pais Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 07 Apr 2011 09:46:15 -0000 Hi, I've looked up that line in the specific_fns/model_free/mf_minimise.py file, and it looks like you are using an older version of relax. Could you copy the output of: $ relax --info This looks like an ancient bug that was eliminated a long, long time ago. Cheers, Edward On 6 April 2011 19:51, Tiago Pais wrote: > I used the expression like this: > grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], inc=3D[1, 11= , 11]) > > But I get the following error: > Unconstrained grid search size: 121 (constraints may decrease this size). > > Traceback (most recent call last): > =A0File "/usr/local/bin/relax", line 418, in > =A0 =A0Relax() > =A0File "/usr/local/bin/relax", line 127, in __init__ > =A0 =A0self.interpreter.run(self.script_file) > =A0File "/usr/local/relax/prompt/interpreter.py", line 276, in run > =A0 =A0return run_script(intro=3Dself.__intro_string, local=3Dself.local, > script_file=3Dscript_file, quit=3Dself.__quit_flag, > show_script=3Dself.__show_script, raise_relax_error=3Dself.__raise_relax_= error) > =A0File "/usr/local/relax/prompt/interpreter.py", line 537, in run_script > =A0 =A0return console.interact(intro, local, script_file, quit, > show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) > =A0File "/usr/local/relax/prompt/interpreter.py", line 433, in > interact_script > =A0 =A0execfile(script_file, local) > =A0File "mf_multimodel_m5S2f0111.py", line 82, in > =A0 =A0grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], inc=3D[= 1, 11, 11]) > =A0File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_sear= ch > =A0 =A0minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, > constraints=3Dconstraints, verbosity=3Dverbosity) > =A0File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_sea= rch > =A0 =A0grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, constraints= =3Dconstraints, > verbosity=3Dverbosity) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 4= 79, > in grid_search > =A0 =A0self.minimise(min_algor=3D'grid', lower=3Dlower, upper=3Dupper, in= c=3Dinc, > constraints=3Dconstraints, verbosity=3Dverbosity, sim_index=3Dsim_index) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 9= 22, > in minimise > =A0 =A0min_options =3D self.grid_search_config(num_params, spin=3Dspin, > lower=3Dlower, upper=3Dupper, inc=3Dinc, scaling_matrix=3Dscaling_matrix) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 5= 54, > in grid_search_config > =A0 =A0self.grid_search_config_fin(min_options, lower, upper, scaling_mat= rix) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 6= 31, > in grid_search_config_fin > =A0 =A0for i in xrange(n): > NameError: global name 'n' is not defined > > > Any ideas? > > Cheers > Tiago > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Abril de 2011 18:05 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > These match the parameters as listed in the help for the > model_free.select_model() user function. =A0The grid search arrays match > the parameter arrays. > > Regards, > > Edward > > > On 6 April 2011 18:54, Tiago Pais wrote: >> Ok, >> Im sorry to insist but I am probably missing something here. How do I > state >> which bound goes with which parameter? That is, which position in the > array >> bound corresponds to the S2f parameter? >> Regards. >> TP >> >> -----Original Message----- >> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On >> Behalf Of Edward d'Auvergne >> Sent: quarta-feira, 6 de Abril de 2011 17:42 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> That is roughly correct. =A0Just set the lower and upper bound to 0.111 >> and set the number of increments for that parameter to 1. =A0Then it is >> like a grid search without S2f being present, or being fixed to 0.111. >> >> Regards, >> >> Edward >> >> >> >> On 6 April 2011 18:38, Tiago Pais wrote: >>> Hi Ed, >>> Thanks for the quick reply. >>> Let's see if I understand your suggestion. For example, the >> mf_multimodel.py >>> sample script performs a grid search minimization using the grid_search >>> function. So if I insert an array of upper and lower bounds for the >>> parameters in the model I can constrain the interval of possible result= s, >>> correct? If so, what is the sequence for the parameters in the array? >>> TP >>> >>> >>> >>> -----Original Message----- >>> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>> To: Tiago Pais >>> Cc: relax-users@domain.hid >>> Subject: Re: How to set S2f to 0.111? >>> >>> Hi, >>> >>> Unfortunately, there is no ability to fix one of the model-free >>> parameters during optimisation in relax yet. =A0This is something that >>> has been requested one or two times over the years. =A0This is >>> complicated as the gradients and Hessians (first and second partial >>> derivates) need to be modified with this in mind, as the curvature of >>> the space changes. =A0The fixed parameter is not part of the gradient o= r >>> Hessian, and has to be removed. =A0This really complicates the target >>> function, gradient, and Hessian and, due to the low demand, has not >>> been implemented. >>> >>> Are you able to optimise this parameter and see if you get 0.111? =A0An= d >>> are you able to extract the timescale of this process (the methyl >>> group rotamer jumps)? =A0From memory, someone has optimsed these models >>> using a grid search. =A0This coarse optimisation can be performed in >>> relax as you are able to specify the fine details of the grid search. >>> It is slower, but will do the job. =A0You could even implement a zoomin= g >>> grid search if your scripting skills are up to it to be able to >>> relatively quickly find the parameters to high precision. =A0Anyway, I >>> hope this info helps. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> >>> On 6 April 2011 17:39, Tiago Pais wrote: >>>> Hi, >>>> >>>> I would like to make an analysis of side-chain relaxation data with th= e >>> S2f >>>> parameter (in model 5) set to 0.111. >>>> >>>> Is it possible to do this with RELAX? How? >>>> >>>> Thanks in advance. >>>> >>>> Cheers >>>> >>>> Tiago P >>>> >>>> >>>> >>>> ************************************** >>>> >>>> Tiago Pais, PhD. student >>>> >>>> Cell Physiology & NMR >>>> >>>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>>> >>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-users mailing list >>>> relax-users@domain.hid >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-users >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > From tpais@domain.hid Thu Apr 07 12:04:32 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7m4f-0004G5-5F for relax-users@domain.hid; Thu, 07 Apr 2011 12:04:32 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail3.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7m4e-0004Fz-TN for relax-users@domain.hid; Thu, 07 Apr 2011 12:04:25 +0200 Received: from mail3.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail3.itqb.unl.pt (Postfix) with ESMTP id 7C2CFC864E7; Thu, 7 Apr 2011 11:04:23 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail3.itqb.unl.pt (Postfix) with ESMTP id 1D747C86418; Thu, 7 Apr 2011 11:04:23 +0100 (WEST) From: "Tiago Pais" To: "'Edward d'Auvergne'" References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid><78F8FACF15244E5DB30D23776CF896D8@domain.hid> Subject: RE: How to set S2f to 0.111? Date: Thu, 7 Apr 2011 11:04:24 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Mailer: Microsoft Office Outlook 11 thread-index: Acv1CJgRpFcXnR2DQfCGaqAU+HnQggAAhGiQ In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 X-Virus-Scanned: ClamAV using ClamSMTP Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 07 Apr 2011 10:04:32 -0000 It's relax 1.3.4 Actually the command "$ relax --info" is not producing any info. -----Original Message----- From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On Behalf Of Edward d'Auvergne Sent: quinta-feira, 7 de Abril de 2011 10:46 To: Tiago Pais Cc: relax-users@domain.hid Subject: Re: How to set S2f to 0.111? Hi, I've looked up that line in the specific_fns/model_free/mf_minimise.py file, and it looks like you are using an older version of relax. Could you copy the output of: $ relax --info This looks like an ancient bug that was eliminated a long, long time = ago. Cheers, Edward On 6 April 2011 19:51, Tiago Pais wrote: > I used the expression like this: > grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], inc=3D[1, = 11, 11]) > > But I get the following error: > Unconstrained grid search size: 121 (constraints may decrease this = size). > > Traceback (most recent call last): > =A0File "/usr/local/bin/relax", line 418, in > =A0 =A0Relax() > =A0File "/usr/local/bin/relax", line 127, in __init__ > =A0 =A0self.interpreter.run(self.script_file) > =A0File "/usr/local/relax/prompt/interpreter.py", line 276, in run > =A0 =A0return run_script(intro=3Dself.__intro_string, = local=3Dself.local, > script_file=3Dscript_file, quit=3Dself.__quit_flag, > show_script=3Dself.__show_script, raise_relax_error=3Dself.__raise_relax_error) > =A0File "/usr/local/relax/prompt/interpreter.py", line 537, in = run_script > =A0 =A0return console.interact(intro, local, script_file, quit, > show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) > =A0File "/usr/local/relax/prompt/interpreter.py", line 433, in > interact_script > =A0 =A0execfile(script_file, local) > =A0File "mf_multimodel_m5S2f0111.py", line 82, in > =A0 =A0grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], = inc=3D[1, 11, 11]) > =A0File "/usr/local/relax/prompt/minimisation.py", line 156, in = grid_search > =A0 =A0minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, > constraints=3Dconstraints, verbosity=3Dverbosity) > =A0File "/usr/local/relax/generic_fns/minimise.py", line 191, in = grid_search > =A0 =A0grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, = constraints=3Dconstraints, > verbosity=3Dverbosity) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 479, > in grid_search > =A0 =A0self.minimise(min_algor=3D'grid', lower=3Dlower, upper=3Dupper, = inc=3Dinc, > constraints=3Dconstraints, verbosity=3Dverbosity, = sim_index=3Dsim_index) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 922, > in minimise > =A0 =A0min_options =3D self.grid_search_config(num_params, = spin=3Dspin, > lower=3Dlower, upper=3Dupper, inc=3Dinc, = scaling_matrix=3Dscaling_matrix) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 554, > in grid_search_config > =A0 =A0self.grid_search_config_fin(min_options, lower, upper, = scaling_matrix) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 631, > in grid_search_config_fin > =A0 =A0for i in xrange(n): > NameError: global name 'n' is not defined > > > Any ideas? > > Cheers > Tiago > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Abril de 2011 18:05 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > These match the parameters as listed in the help for the > model_free.select_model() user function. =A0The grid search arrays = match > the parameter arrays. > > Regards, > > Edward > > > On 6 April 2011 18:54, Tiago Pais wrote: >> Ok, >> Im sorry to insist but I am probably missing something here. How do I > state >> which bound goes with which parameter? That is, which position in the > array >> bound corresponds to the S2f parameter? >> Regards. >> TP >> >> -----Original Message----- >> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On >> Behalf Of Edward d'Auvergne >> Sent: quarta-feira, 6 de Abril de 2011 17:42 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> That is roughly correct. =A0Just set the lower and upper bound to = 0.111 >> and set the number of increments for that parameter to 1. =A0Then it = is >> like a grid search without S2f being present, or being fixed to = 0.111. >> >> Regards, >> >> Edward >> >> >> >> On 6 April 2011 18:38, Tiago Pais wrote: >>> Hi Ed, >>> Thanks for the quick reply. >>> Let's see if I understand your suggestion. For example, the >> mf_multimodel.py >>> sample script performs a grid search minimization using the = grid_search >>> function. So if I insert an array of upper and lower bounds for the >>> parameters in the model I can constrain the interval of possible results, >>> correct? If so, what is the sequence for the parameters in the = array? >>> TP >>> >>> >>> >>> -----Original Message----- >>> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>> To: Tiago Pais >>> Cc: relax-users@domain.hid >>> Subject: Re: How to set S2f to 0.111? >>> >>> Hi, >>> >>> Unfortunately, there is no ability to fix one of the model-free >>> parameters during optimisation in relax yet. =A0This is something = that >>> has been requested one or two times over the years. =A0This is >>> complicated as the gradients and Hessians (first and second partial >>> derivates) need to be modified with this in mind, as the curvature = of >>> the space changes. =A0The fixed parameter is not part of the = gradient or >>> Hessian, and has to be removed. =A0This really complicates the = target >>> function, gradient, and Hessian and, due to the low demand, has not >>> been implemented. >>> >>> Are you able to optimise this parameter and see if you get 0.111? = =A0And >>> are you able to extract the timescale of this process (the methyl >>> group rotamer jumps)? =A0From memory, someone has optimsed these = models >>> using a grid search. =A0This coarse optimisation can be performed in >>> relax as you are able to specify the fine details of the grid = search. >>> It is slower, but will do the job. =A0You could even implement a = zooming >>> grid search if your scripting skills are up to it to be able to >>> relatively quickly find the parameters to high precision. =A0Anyway, = I >>> hope this info helps. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> >>> On 6 April 2011 17:39, Tiago Pais wrote: >>>> Hi, >>>> >>>> I would like to make an analysis of side-chain relaxation data with = the >>> S2f >>>> parameter (in model 5) set to 0.111. >>>> >>>> Is it possible to do this with RELAX? How? >>>> >>>> Thanks in advance. >>>> >>>> Cheers >>>> >>>> Tiago P >>>> >>>> >>>> >>>> ************************************** >>>> >>>> Tiago Pais, PhD. student >>>> >>>> Cell Physiology & NMR >>>> >>>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>>> >>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-users mailing list >>>> relax-users@domain.hid >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-users >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6021 (20110407) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6021 (20110407) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From tpais@domain.hid Thu Apr 07 13:09:50 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7n5r-0002sX-6B for relax-users@domain.hid; Thu, 07 Apr 2011 13:09:50 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail3.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7n5q-0002sR-Ug for relax-users@domain.hid; Thu, 07 Apr 2011 13:09:43 +0200 Received: from mail3.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail3.itqb.unl.pt (Postfix) with ESMTP id D8513C8614A; Thu, 7 Apr 2011 12:09:41 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail3.itqb.unl.pt (Postfix) with ESMTP id 9818AC86135; Thu, 7 Apr 2011 12:09:41 +0100 (WEST) From: "Tiago Pais" To: "'Edward d'Auvergne'" References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid><78F8FACF15244E5DB30D23776CF896D8@domain.hid> Subject: RE: How to set S2f to 0.111? - SOLVED with 1.3.8 Date: Thu, 7 Apr 2011 12:09:42 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Mailer: Microsoft Office Outlook 11 thread-index: Acv1CJgRpFcXnR2DQfCGaqAU+HnQggACnpgg In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 X-Virus-Scanned: ClamAV using ClamSMTP Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 07 Apr 2011 11:09:50 -0000 I have now also running the 1.3.8 version and the problem seems to have disappeared. Took me some time to use this version because the column numbering has changed, now columns start at number one! Important! ;-) I hope now this goes well. Thanks once more for your valuable help. Cheers Tiago -----Original Message----- From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On Behalf Of Edward d'Auvergne Sent: quinta-feira, 7 de Abril de 2011 10:46 To: Tiago Pais Cc: relax-users@domain.hid Subject: Re: How to set S2f to 0.111? Hi, I've looked up that line in the specific_fns/model_free/mf_minimise.py file, and it looks like you are using an older version of relax. Could you copy the output of: $ relax --info This looks like an ancient bug that was eliminated a long, long time = ago. Cheers, Edward On 6 April 2011 19:51, Tiago Pais wrote: > I used the expression like this: > grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], inc=3D[1, = 11, 11]) > > But I get the following error: > Unconstrained grid search size: 121 (constraints may decrease this = size). > > Traceback (most recent call last): > =A0File "/usr/local/bin/relax", line 418, in > =A0 =A0Relax() > =A0File "/usr/local/bin/relax", line 127, in __init__ > =A0 =A0self.interpreter.run(self.script_file) > =A0File "/usr/local/relax/prompt/interpreter.py", line 276, in run > =A0 =A0return run_script(intro=3Dself.__intro_string, = local=3Dself.local, > script_file=3Dscript_file, quit=3Dself.__quit_flag, > show_script=3Dself.__show_script, raise_relax_error=3Dself.__raise_relax_error) > =A0File "/usr/local/relax/prompt/interpreter.py", line 537, in = run_script > =A0 =A0return console.interact(intro, local, script_file, quit, > show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) > =A0File "/usr/local/relax/prompt/interpreter.py", line 433, in > interact_script > =A0 =A0execfile(script_file, local) > =A0File "mf_multimodel_m5S2f0111.py", line 82, in > =A0 =A0grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], = inc=3D[1, 11, 11]) > =A0File "/usr/local/relax/prompt/minimisation.py", line 156, in = grid_search > =A0 =A0minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, > constraints=3Dconstraints, verbosity=3Dverbosity) > =A0File "/usr/local/relax/generic_fns/minimise.py", line 191, in = grid_search > =A0 =A0grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, = constraints=3Dconstraints, > verbosity=3Dverbosity) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 479, > in grid_search > =A0 =A0self.minimise(min_algor=3D'grid', lower=3Dlower, upper=3Dupper, = inc=3Dinc, > constraints=3Dconstraints, verbosity=3Dverbosity, = sim_index=3Dsim_index) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 922, > in minimise > =A0 =A0min_options =3D self.grid_search_config(num_params, = spin=3Dspin, > lower=3Dlower, upper=3Dupper, inc=3Dinc, = scaling_matrix=3Dscaling_matrix) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 554, > in grid_search_config > =A0 =A0self.grid_search_config_fin(min_options, lower, upper, = scaling_matrix) > =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 631, > in grid_search_config_fin > =A0 =A0for i in xrange(n): > NameError: global name 'n' is not defined > > > Any ideas? > > Cheers > Tiago > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Abril de 2011 18:05 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > These match the parameters as listed in the help for the > model_free.select_model() user function. =A0The grid search arrays = match > the parameter arrays. > > Regards, > > Edward > > > On 6 April 2011 18:54, Tiago Pais wrote: >> Ok, >> Im sorry to insist but I am probably missing something here. How do I > state >> which bound goes with which parameter? That is, which position in the > array >> bound corresponds to the S2f parameter? >> Regards. >> TP >> >> -----Original Message----- >> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On >> Behalf Of Edward d'Auvergne >> Sent: quarta-feira, 6 de Abril de 2011 17:42 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> That is roughly correct. =A0Just set the lower and upper bound to = 0.111 >> and set the number of increments for that parameter to 1. =A0Then it = is >> like a grid search without S2f being present, or being fixed to = 0.111. >> >> Regards, >> >> Edward >> >> >> >> On 6 April 2011 18:38, Tiago Pais wrote: >>> Hi Ed, >>> Thanks for the quick reply. >>> Let's see if I understand your suggestion. For example, the >> mf_multimodel.py >>> sample script performs a grid search minimization using the = grid_search >>> function. So if I insert an array of upper and lower bounds for the >>> parameters in the model I can constrain the interval of possible results, >>> correct? If so, what is the sequence for the parameters in the = array? >>> TP >>> >>> >>> >>> -----Original Message----- >>> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>> To: Tiago Pais >>> Cc: relax-users@domain.hid >>> Subject: Re: How to set S2f to 0.111? >>> >>> Hi, >>> >>> Unfortunately, there is no ability to fix one of the model-free >>> parameters during optimisation in relax yet. =A0This is something = that >>> has been requested one or two times over the years. =A0This is >>> complicated as the gradients and Hessians (first and second partial >>> derivates) need to be modified with this in mind, as the curvature = of >>> the space changes. =A0The fixed parameter is not part of the = gradient or >>> Hessian, and has to be removed. =A0This really complicates the = target >>> function, gradient, and Hessian and, due to the low demand, has not >>> been implemented. >>> >>> Are you able to optimise this parameter and see if you get 0.111? = =A0And >>> are you able to extract the timescale of this process (the methyl >>> group rotamer jumps)? =A0From memory, someone has optimsed these = models >>> using a grid search. =A0This coarse optimisation can be performed in >>> relax as you are able to specify the fine details of the grid = search. >>> It is slower, but will do the job. =A0You could even implement a = zooming >>> grid search if your scripting skills are up to it to be able to >>> relatively quickly find the parameters to high precision. =A0Anyway, = I >>> hope this info helps. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> >>> On 6 April 2011 17:39, Tiago Pais wrote: >>>> Hi, >>>> >>>> I would like to make an analysis of side-chain relaxation data with = the >>> S2f >>>> parameter (in model 5) set to 0.111. >>>> >>>> Is it possible to do this with RELAX? How? >>>> >>>> Thanks in advance. >>>> >>>> Cheers >>>> >>>> Tiago P >>>> >>>> >>>> >>>> ************************************** >>>> >>>> Tiago Pais, PhD. student >>>> >>>> Cell Physiology & NMR >>>> >>>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>>> >>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-users mailing list >>>> relax-users@domain.hid >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-users >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6021 (20110407) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6021 (20110407) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From edward.dauvergne@domain.hid Thu Apr 07 13:12:49 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7n8j-0003G0-HP for relax-users@domain.hid; Thu, 07 Apr 2011 13:12:49 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-3.6 required=3.3 tests=BAYES_00,RCVD_IN_DNSWL_LOW autolearn=ham version=3.2.5 Received: from mail-vw0-f51.google.com ([209.85.212.51]) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7n8j-0003Eq-Ab for relax-users@domain.hid; Thu, 07 Apr 2011 13:12:41 +0200 Received: by vws20 with SMTP id 20so1745132vws.10 for ; Thu, 07 Apr 2011 04:12:19 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; bh=L4XtYtfVMIj0qqV4iLKrlNaatxsY3XgYmWBUWg8nASk=; b=LJeCa2Rv9WUaExjEeC49tYhA535AXTm3mgiRzAFe/bun69Ue6fpe0GnklYHdrnk38b PDNi21hk62nVO6gMO5RtRD5jdf7DC+Tg3XEZkSEV9TUJlyLmM81XmbDbzUiA52r8A+Gz aZ0oAxKCrw9q3o8k5fenUNYAee5HXkgYD9A6M= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; b=fH2afu/eZFt9EFxTKaFBLxxA+k7oOIdPzHb/eQNFF5ak5EL9lbK3aNrzsJT3s9j5kb IkFZcH2/E4CbIUBWbk7aBFqRymHTSpew8SI/8czLdz/TU5dHd/aMbwKdL2TGR7TzQ1wf 4/bm+Exfj609ezZaGAlMTNk+PX8npWF9+4LA0= MIME-Version: 1.0 Received: by 10.52.69.240 with SMTP id h16mr1045722vdu.214.1302174738713; Thu, 07 Apr 2011 04:12:18 -0700 (PDT) Sender: edward.dauvergne@domain.hid Received: by 10.52.164.101 with HTTP; Thu, 7 Apr 2011 04:12:18 -0700 (PDT) In-Reply-To: References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> <78F8FACF15244E5DB30D23776CF896D8@domain.hid> Date: Thu, 7 Apr 2011 13:12:18 +0200 X-Google-Sender-Auth: rdy6KZafGQJryvQUHjmYQiWzefY Message-ID: Subject: Re: How to set S2f to 0.111? From: "Edward d'Auvergne" To: Tiago Pais Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 07 Apr 2011 11:12:49 -0000 Hi, This really looks like a bug I fixed a long time ago, although unfortunately I cannot find it at the moment. Are you able to try out the latest version of relax, version 1.3.10 from http://www.nmr-relax.com/download.html? The grid search code of minfx (https://gna.org/projects/minfx/), which is now bundled with relax, is now radically different to that of 1.3.4 and is much more powerful. Regards, Edward On 7 April 2011 12:04, Tiago Pais wrote: > It's relax 1.3.4 > Actually the command "$ relax --info" is not producing any info. > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On > Behalf Of Edward d'Auvergne > Sent: quinta-feira, 7 de Abril de 2011 10:46 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > I've looked up that line in the specific_fns/model_free/mf_minimise.py > file, and it looks like you are using an older version of relax. > Could you copy the output of: > > $ relax --info > > This looks like an ancient bug that was eliminated a long, long time ago. > > Cheers, > > Edward > > > > > On 6 April 2011 19:51, Tiago Pais wrote: >> I used the expression like this: >> grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], inc=3D[1, 1= 1, 11]) >> >> But I get the following error: >> Unconstrained grid search size: 121 (constraints may decrease this size)= . >> >> Traceback (most recent call last): >> =A0File "/usr/local/bin/relax", line 418, in >> =A0 =A0Relax() >> =A0File "/usr/local/bin/relax", line 127, in __init__ >> =A0 =A0self.interpreter.run(self.script_file) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 276, in run >> =A0 =A0return run_script(intro=3Dself.__intro_string, local=3Dself.local= , >> script_file=3Dscript_file, quit=3Dself.__quit_flag, >> show_script=3Dself.__show_script, > raise_relax_error=3Dself.__raise_relax_error) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 537, in run_scrip= t >> =A0 =A0return console.interact(intro, local, script_file, quit, >> show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 433, in >> interact_script >> =A0 =A0execfile(script_file, local) >> =A0File "mf_multimodel_m5S2f0111.py", line 82, in >> =A0 =A0grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], inc=3D= [1, 11, 11]) >> =A0File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_sea= rch >> =A0 =A0minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, >> constraints=3Dconstraints, verbosity=3Dverbosity) >> =A0File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_se= arch >> =A0 =A0grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, constraints= =3Dconstraints, >> verbosity=3Dverbosity) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 479, >> in grid_search >> =A0 =A0self.minimise(min_algor=3D'grid', lower=3Dlower, upper=3Dupper, i= nc=3Dinc, >> constraints=3Dconstraints, verbosity=3Dverbosity, sim_index=3Dsim_index) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 922, >> in minimise >> =A0 =A0min_options =3D self.grid_search_config(num_params, spin=3Dspin, >> lower=3Dlower, upper=3Dupper, inc=3Dinc, scaling_matrix=3Dscaling_matrix= ) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 554, >> in grid_search_config >> =A0 =A0self.grid_search_config_fin(min_options, lower, upper, scaling_ma= trix) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 631, >> in grid_search_config_fin >> =A0 =A0for i in xrange(n): >> NameError: global name 'n' is not defined >> >> >> Any ideas? >> >> Cheers >> Tiago >> >> -----Original Message----- >> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On >> Behalf Of Edward d'Auvergne >> Sent: quarta-feira, 6 de Abril de 2011 18:05 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> These match the parameters as listed in the help for the >> model_free.select_model() user function. =A0The grid search arrays match >> the parameter arrays. >> >> Regards, >> >> Edward >> >> >> On 6 April 2011 18:54, Tiago Pais wrote: >>> Ok, >>> Im sorry to insist but I am probably missing something here. How do I >> state >>> which bound goes with which parameter? That is, which position in the >> array >>> bound corresponds to the S2f parameter? >>> Regards. >>> TP >>> >>> -----Original Message----- >>> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On >>> Behalf Of Edward d'Auvergne >>> Sent: quarta-feira, 6 de Abril de 2011 17:42 >>> To: Tiago Pais >>> Cc: relax-users@domain.hid >>> Subject: Re: How to set S2f to 0.111? >>> >>> Hi, >>> >>> That is roughly correct. =A0Just set the lower and upper bound to 0.111 >>> and set the number of increments for that parameter to 1. =A0Then it is >>> like a grid search without S2f being present, or being fixed to 0.111. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> On 6 April 2011 18:38, Tiago Pais wrote: >>>> Hi Ed, >>>> Thanks for the quick reply. >>>> Let's see if I understand your suggestion. For example, the >>> mf_multimodel.py >>>> sample script performs a grid search minimization using the grid_searc= h >>>> function. So if I insert an array of upper and lower bounds for the >>>> parameters in the model I can constrain the interval of possible > results, >>>> correct? If so, what is the sequence for the parameters in the array? >>>> TP >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >>>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>>> To: Tiago Pais >>>> Cc: relax-users@domain.hid >>>> Subject: Re: How to set S2f to 0.111? >>>> >>>> Hi, >>>> >>>> Unfortunately, there is no ability to fix one of the model-free >>>> parameters during optimisation in relax yet. =A0This is something that >>>> has been requested one or two times over the years. =A0This is >>>> complicated as the gradients and Hessians (first and second partial >>>> derivates) need to be modified with this in mind, as the curvature of >>>> the space changes. =A0The fixed parameter is not part of the gradient = or >>>> Hessian, and has to be removed. =A0This really complicates the target >>>> function, gradient, and Hessian and, due to the low demand, has not >>>> been implemented. >>>> >>>> Are you able to optimise this parameter and see if you get 0.111? =A0A= nd >>>> are you able to extract the timescale of this process (the methyl >>>> group rotamer jumps)? =A0From memory, someone has optimsed these model= s >>>> using a grid search. =A0This coarse optimisation can be performed in >>>> relax as you are able to specify the fine details of the grid search. >>>> It is slower, but will do the job. =A0You could even implement a zoomi= ng >>>> grid search if your scripting skills are up to it to be able to >>>> relatively quickly find the parameters to high precision. =A0Anyway, I >>>> hope this info helps. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> >>>> >>>> On 6 April 2011 17:39, Tiago Pais wrote: >>>>> Hi, >>>>> >>>>> I would like to make an analysis of side-chain relaxation data with t= he >>>> S2f >>>>> parameter (in model 5) set to 0.111. >>>>> >>>>> Is it possible to do this with RELAX? How? >>>>> >>>>> Thanks in advance. >>>>> >>>>> Cheers >>>>> >>>>> Tiago P >>>>> >>>>> >>>>> >>>>> ************************************** >>>>> >>>>> Tiago Pais, PhD. student >>>>> >>>>> Cell Physiology & NMR >>>>> >>>>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>>>> >>>>> >>>>> >>>>> __________ Information from ESET NOD32 Antivirus, version of virus >>>> signature >>>>> database 6019 (20110406) __________ >>>>> >>>>> The message was checked by ESET NOD32 Antivirus. >>>>> >>>>> http://www.eset.com >>>>> >>>>> _______________________________________________ >>>>> relax (http://nmr-relax.com) >>>>> >>>>> This is the relax-users mailing list >>>>> relax-users@domain.hid >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-users >>>>> >>>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6021 (20110407) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6021 (20110407) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > From edward.dauvergne@domain.hid Thu Apr 07 13:15:53 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q7nBi-0003eA-5F for relax-users@domain.hid; Thu, 07 Apr 2011 13:15:53 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-3.6 required=3.3 tests=BAYES_00,RCVD_IN_DNSWL_LOW autolearn=ham version=3.2.5 Received: from mail-vw0-f51.google.com ([209.85.212.51]) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q7nBh-0003ck-U2 for relax-users@domain.hid; Thu, 07 Apr 2011 13:15:46 +0200 Received: by vws20 with SMTP id 20so1746668vws.10 for ; Thu, 07 Apr 2011 04:15:24 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; bh=FePa0O3T4qE3DVpqvEAeFWhCzk94ZU0NceXu5oLCEyc=; b=rlN+6EsASAtkK8HNjtv0DcwurD8fB8qZTEJPa4UwiiczVw4bsP/Rk5FowCyyVF2RcU IPfwVFf134QZ669WiiorCGOOx9JM24rZT/R9bQrcT1ym0amo8nYYQcv3ssSDjcNdIg/X doSYn1Ic5yi81vfEGsS9cw/78rdIc06JaCJag= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; b=Zx9PI9hsoQd7jWV24HVqxu/ia0wz7jZWjfV7nJcJ3njklA8SycawVU5jDFSge3g+xC vKMvwhBDLCehTzDhHqLaGJRocCq3WfiYPV/yum5V1UFiPV/itsGxSbhOtQSr/20jhmSB 6XkVZnxXYKaGOqS5iqRUYBdNwrr8X/2QVBEx0= MIME-Version: 1.0 Received: by 10.52.66.241 with SMTP id i17mr1068939vdt.54.1302174923602; Thu, 07 Apr 2011 04:15:23 -0700 (PDT) Sender: edward.dauvergne@domain.hid Received: by 10.52.164.101 with HTTP; Thu, 7 Apr 2011 04:15:23 -0700 (PDT) In-Reply-To: References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> <78F8FACF15244E5DB30D23776CF896D8@domain.hid> Date: Thu, 7 Apr 2011 13:15:23 +0200 X-Google-Sender-Auth: 7ekwbNcxo_oK9agKAw74p8TNMiw Message-ID: Subject: Re: How to set S2f to 0.111? - SOLVED with 1.3.8 From: "Edward d'Auvergne" To: Tiago Pais Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 07 Apr 2011 11:15:53 -0000 Ah, right. I did fix that bug! I thought so :) Ok, if you have any problems, don't hesitate to ask. Bye, Edward On 7 April 2011 13:09, Tiago Pais wrote: > I have now also running the 1.3.8 version and the problem seems to have > disappeared. Took me some time to use this version because the column > numbering has changed, now columns start at number one! Important! ;-) > > I hope now this goes well. > > Thanks once more for your valuable help. > Cheers > Tiago > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On > Behalf Of Edward d'Auvergne > Sent: quinta-feira, 7 de Abril de 2011 10:46 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > I've looked up that line in the specific_fns/model_free/mf_minimise.py > file, and it looks like you are using an older version of relax. > Could you copy the output of: > > $ relax --info > > This looks like an ancient bug that was eliminated a long, long time ago. > > Cheers, > > Edward > > > > > On 6 April 2011 19:51, Tiago Pais wrote: >> I used the expression like this: >> grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], inc=3D[1, 1= 1, 11]) >> >> But I get the following error: >> Unconstrained grid search size: 121 (constraints may decrease this size)= . >> >> Traceback (most recent call last): >> =A0File "/usr/local/bin/relax", line 418, in >> =A0 =A0Relax() >> =A0File "/usr/local/bin/relax", line 127, in __init__ >> =A0 =A0self.interpreter.run(self.script_file) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 276, in run >> =A0 =A0return run_script(intro=3Dself.__intro_string, local=3Dself.local= , >> script_file=3Dscript_file, quit=3Dself.__quit_flag, >> show_script=3Dself.__show_script, > raise_relax_error=3Dself.__raise_relax_error) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 537, in run_scrip= t >> =A0 =A0return console.interact(intro, local, script_file, quit, >> show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 433, in >> interact_script >> =A0 =A0execfile(script_file, local) >> =A0File "mf_multimodel_m5S2f0111.py", line 82, in >> =A0 =A0grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], inc=3D= [1, 11, 11]) >> =A0File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_sea= rch >> =A0 =A0minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, >> constraints=3Dconstraints, verbosity=3Dverbosity) >> =A0File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_se= arch >> =A0 =A0grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, constraints= =3Dconstraints, >> verbosity=3Dverbosity) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 479, >> in grid_search >> =A0 =A0self.minimise(min_algor=3D'grid', lower=3Dlower, upper=3Dupper, i= nc=3Dinc, >> constraints=3Dconstraints, verbosity=3Dverbosity, sim_index=3Dsim_index) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 922, >> in minimise >> =A0 =A0min_options =3D self.grid_search_config(num_params, spin=3Dspin, >> lower=3Dlower, upper=3Dupper, inc=3Dinc, scaling_matrix=3Dscaling_matrix= ) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 554, >> in grid_search_config >> =A0 =A0self.grid_search_config_fin(min_options, lower, upper, scaling_ma= trix) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line = 631, >> in grid_search_config_fin >> =A0 =A0for i in xrange(n): >> NameError: global name 'n' is not defined >> >> >> Any ideas? >> >> Cheers >> Tiago >> >> -----Original Message----- >> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On >> Behalf Of Edward d'Auvergne >> Sent: quarta-feira, 6 de Abril de 2011 18:05 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> These match the parameters as listed in the help for the >> model_free.select_model() user function. =A0The grid search arrays match >> the parameter arrays. >> >> Regards, >> >> Edward >> >> >> On 6 April 2011 18:54, Tiago Pais wrote: >>> Ok, >>> Im sorry to insist but I am probably missing something here. How do I >> state >>> which bound goes with which parameter? That is, which position in the >> array >>> bound corresponds to the S2f parameter? >>> Regards. >>> TP >>> >>> -----Original Message----- >>> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On >>> Behalf Of Edward d'Auvergne >>> Sent: quarta-feira, 6 de Abril de 2011 17:42 >>> To: Tiago Pais >>> Cc: relax-users@domain.hid >>> Subject: Re: How to set S2f to 0.111? >>> >>> Hi, >>> >>> That is roughly correct. =A0Just set the lower and upper bound to 0.111 >>> and set the number of increments for that parameter to 1. =A0Then it is >>> like a grid search without S2f being present, or being fixed to 0.111. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> On 6 April 2011 18:38, Tiago Pais wrote: >>>> Hi Ed, >>>> Thanks for the quick reply. >>>> Let's see if I understand your suggestion. For example, the >>> mf_multimodel.py >>>> sample script performs a grid search minimization using the grid_searc= h >>>> function. So if I insert an array of upper and lower bounds for the >>>> parameters in the model I can constrain the interval of possible > results, >>>> correct? If so, what is the sequence for the parameters in the array? >>>> TP >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >>>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>>> To: Tiago Pais >>>> Cc: relax-users@domain.hid >>>> Subject: Re: How to set S2f to 0.111? >>>> >>>> Hi, >>>> >>>> Unfortunately, there is no ability to fix one of the model-free >>>> parameters during optimisation in relax yet. =A0This is something that >>>> has been requested one or two times over the years. =A0This is >>>> complicated as the gradients and Hessians (first and second partial >>>> derivates) need to be modified with this in mind, as the curvature of >>>> the space changes. =A0The fixed parameter is not part of the gradient = or >>>> Hessian, and has to be removed. =A0This really complicates the target >>>> function, gradient, and Hessian and, due to the low demand, has not >>>> been implemented. >>>> >>>> Are you able to optimise this parameter and see if you get 0.111? =A0A= nd >>>> are you able to extract the timescale of this process (the methyl >>>> group rotamer jumps)? =A0From memory, someone has optimsed these model= s >>>> using a grid search. =A0This coarse optimisation can be performed in >>>> relax as you are able to specify the fine details of the grid search. >>>> It is slower, but will do the job. =A0You could even implement a zoomi= ng >>>> grid search if your scripting skills are up to it to be able to >>>> relatively quickly find the parameters to high precision. =A0Anyway, I >>>> hope this info helps. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> >>>> >>>> On 6 April 2011 17:39, Tiago Pais wrote: >>>>> Hi, >>>>> >>>>> I would like to make an analysis of side-chain relaxation data with t= he >>>> S2f >>>>> parameter (in model 5) set to 0.111. >>>>> >>>>> Is it possible to do this with RELAX? How? >>>>> >>>>> Thanks in advance. >>>>> >>>>> Cheers >>>>> >>>>> Tiago P >>>>> >>>>> >>>>> >>>>> ************************************** >>>>> >>>>> Tiago Pais, PhD. student >>>>> >>>>> Cell Physiology & NMR >>>>> >>>>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>>>> >>>>> >>>>> >>>>> __________ Information from ESET NOD32 Antivirus, version of virus >>>> signature >>>>> database 6019 (20110406) __________ >>>>> >>>>> The message was checked by ESET NOD32 Antivirus. >>>>> >>>>> http://www.eset.com >>>>> >>>>> _______________________________________________ >>>>> relax (http://nmr-relax.com) >>>>> >>>>> This is the relax-users mailing list >>>>> relax-users@domain.hid >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-users >>>>> >>>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6021 (20110407) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6021 (20110407) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > From tpais@domain.hid Mon Apr 11 12:34:25 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q9ERm-000247-82 for relax-users@domain.hid; Mon, 11 Apr 2011 12:34:25 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail3.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q9ERm-000244-0T for relax-users@domain.hid; Mon, 11 Apr 2011 12:34:18 +0200 Received: from mail3.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail3.itqb.unl.pt (Postfix) with ESMTP id CEDC2C863D0; Mon, 11 Apr 2011 11:34:16 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail3.itqb.unl.pt (Postfix) with ESMTP id AB133C863AB; Mon, 11 Apr 2011 11:34:16 +0100 (WEST) From: "Tiago Pais" To: "'Edward d'Auvergne'" References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid><78F8FACF15244E5DB30D23776CF896D8@domain.hid> Subject: Grid search does not appear to do the job Date: Mon, 11 Apr 2011 11:34:21 +0100 Message-ID: <81DC9F5819CB4D7395FEA1359BB2F040@domain.hid> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Mailer: Microsoft Office Outlook 11 Thread-Index: Acv1FR2aQgVYV/w2Sf6wAvunksnCDQDHeRHg In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 X-Virus-Scanned: ClamAV using ClamSMTP Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 11 Apr 2011 10:34:25 -0000 Hi Edward, I have been trying several combinations but the grid search does not = appear to be doing its job. I have used the following command in the script: "grid_search(lower=3D[0.111, 0, -0.0], upper=3D[0.111, 1.00, 200], = inc=3D[16, 16, 16], verbosity=3D7)" But I keep seeing this during the calculations: "Min f: 3474.82 =20 k: 3860 xk: [ 0.111, 0.066667, -0] fk: nan Increment: array([ 5, 16, 16])=20 Params: array([ 0.111, 1. , Inf]) Min params: array([ 0.111 , 0.06666667, -0. ]) f: nan =20 Min f: 3474.82 =20 k: 3861 xk: [ 0.111, 0.066667, -0] fk: nan Increment: array([ 6, 16, 16])=20 Params: array([ 0.111, 1. , Inf]) Min params: array([ 0.111 , 0.06666667, -0. ]) f: nan =20 " And at the end the tauS is zero for all spins and the S2s is always = close to 1. It appears that the space is not being adequately created... Any suggestion? Thanks Tiago P -----Original Message----- From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On Behalf Of Edward d'Auvergne Sent: quinta-feira, 7 de Abril de 2011 12:15 To: Tiago Pais Cc: relax-users@domain.hid Subject: Re: How to set S2f to 0.111? - SOLVED with 1.3.8 Ah, right. I did fix that bug! I thought so :) Ok, if you have any problems, don't hesitate to ask. Bye, Edward On 7 April 2011 13:09, Tiago Pais wrote: > I have now also running the 1.3.8 version and the problem seems to = have > disappeared. Took me some time to use this version because the column > numbering has changed, now columns start at number one! Important! ;-) > > I hope now this goes well. > > Thanks once more for your valuable help. > Cheers > Tiago > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On > Behalf Of Edward d'Auvergne > Sent: quinta-feira, 7 de Abril de 2011 10:46 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? > > Hi, > > I've looked up that line in the specific_fns/model_free/mf_minimise.py > file, and it looks like you are using an older version of relax. > Could you copy the output of: > > $ relax --info > > This looks like an ancient bug that was eliminated a long, long time = ago. > > Cheers, > > Edward > > > > > On 6 April 2011 19:51, Tiago Pais wrote: >> I used the expression like this: >> grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], = inc=3D[1, 11, 11]) >> >> But I get the following error: >> Unconstrained grid search size: 121 (constraints may decrease this = size). >> >> Traceback (most recent call last): >> =A0File "/usr/local/bin/relax", line 418, in >> =A0 =A0Relax() >> =A0File "/usr/local/bin/relax", line 127, in __init__ >> =A0 =A0self.interpreter.run(self.script_file) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 276, in run >> =A0 =A0return run_script(intro=3Dself.__intro_string, = local=3Dself.local, >> script_file=3Dscript_file, quit=3Dself.__quit_flag, >> show_script=3Dself.__show_script, > raise_relax_error=3Dself.__raise_relax_error) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 537, in = run_script >> =A0 =A0return console.interact(intro, local, script_file, quit, >> show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) >> =A0File "/usr/local/relax/prompt/interpreter.py", line 433, in >> interact_script >> =A0 =A0execfile(script_file, local) >> =A0File "mf_multimodel_m5S2f0111.py", line 82, in >> =A0 =A0grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], = inc=3D[1, 11, 11]) >> =A0File "/usr/local/relax/prompt/minimisation.py", line 156, in = grid_search >> =A0 =A0minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, >> constraints=3Dconstraints, verbosity=3Dverbosity) >> =A0File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_search >> =A0 =A0grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, constraints=3Dconstraints, >> verbosity=3Dverbosity) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 479, >> in grid_search >> =A0 =A0self.minimise(min_algor=3D'grid', lower=3Dlower, = upper=3Dupper, inc=3Dinc, >> constraints=3Dconstraints, verbosity=3Dverbosity, = sim_index=3Dsim_index) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 922, >> in minimise >> =A0 =A0min_options =3D self.grid_search_config(num_params, = spin=3Dspin, >> lower=3Dlower, upper=3Dupper, inc=3Dinc, = scaling_matrix=3Dscaling_matrix) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 554, >> in grid_search_config >> =A0 =A0self.grid_search_config_fin(min_options, lower, upper, = scaling_matrix) >> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line 631, >> in grid_search_config_fin >> =A0 =A0for i in xrange(n): >> NameError: global name 'n' is not defined >> >> >> Any ideas? >> >> Cheers >> Tiago >> >> -----Original Message----- >> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On >> Behalf Of Edward d'Auvergne >> Sent: quarta-feira, 6 de Abril de 2011 18:05 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> These match the parameters as listed in the help for the >> model_free.select_model() user function. =A0The grid search arrays = match >> the parameter arrays. >> >> Regards, >> >> Edward >> >> >> On 6 April 2011 18:54, Tiago Pais wrote: >>> Ok, >>> Im sorry to insist but I am probably missing something here. How do = I >> state >>> which bound goes with which parameter? That is, which position in = the >> array >>> bound corresponds to the S2f parameter? >>> Regards. >>> TP >>> >>> -----Original Message----- >>> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On >>> Behalf Of Edward d'Auvergne >>> Sent: quarta-feira, 6 de Abril de 2011 17:42 >>> To: Tiago Pais >>> Cc: relax-users@domain.hid >>> Subject: Re: How to set S2f to 0.111? >>> >>> Hi, >>> >>> That is roughly correct. =A0Just set the lower and upper bound to = 0.111 >>> and set the number of increments for that parameter to 1. =A0Then it = is >>> like a grid search without S2f being present, or being fixed to = 0.111. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> On 6 April 2011 18:38, Tiago Pais wrote: >>>> Hi Ed, >>>> Thanks for the quick reply. >>>> Let's see if I understand your suggestion. For example, the >>> mf_multimodel.py >>>> sample script performs a grid search minimization using the = grid_search >>>> function. So if I insert an array of upper and lower bounds for the >>>> parameters in the model I can constrain the interval of possible > results, >>>> correct? If so, what is the sequence for the parameters in the = array? >>>> TP >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >>>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>>> To: Tiago Pais >>>> Cc: relax-users@domain.hid >>>> Subject: Re: How to set S2f to 0.111? >>>> >>>> Hi, >>>> >>>> Unfortunately, there is no ability to fix one of the model-free >>>> parameters during optimisation in relax yet. =A0This is something = that >>>> has been requested one or two times over the years. =A0This is >>>> complicated as the gradients and Hessians (first and second partial >>>> derivates) need to be modified with this in mind, as the curvature = of >>>> the space changes. =A0The fixed parameter is not part of the = gradient or >>>> Hessian, and has to be removed. =A0This really complicates the = target >>>> function, gradient, and Hessian and, due to the low demand, has not >>>> been implemented. >>>> >>>> Are you able to optimise this parameter and see if you get 0.111? = =A0And >>>> are you able to extract the timescale of this process (the methyl >>>> group rotamer jumps)? =A0From memory, someone has optimsed these = models >>>> using a grid search. =A0This coarse optimisation can be performed = in >>>> relax as you are able to specify the fine details of the grid = search. >>>> It is slower, but will do the job. =A0You could even implement a = zooming >>>> grid search if your scripting skills are up to it to be able to >>>> relatively quickly find the parameters to high precision. = =A0Anyway, I >>>> hope this info helps. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> >>>> >>>> On 6 April 2011 17:39, Tiago Pais wrote: >>>>> Hi, >>>>> >>>>> I would like to make an analysis of side-chain relaxation data = with the >>>> S2f >>>>> parameter (in model 5) set to 0.111. >>>>> >>>>> Is it possible to do this with RELAX? How? >>>>> >>>>> Thanks in advance. >>>>> >>>>> Cheers >>>>> >>>>> Tiago P >>>>> >>>>> >>>>> >>>>> ************************************** >>>>> >>>>> Tiago Pais, PhD. student >>>>> >>>>> Cell Physiology & NMR >>>>> >>>>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>>>> >>>>> >>>>> >>>>> __________ Information from ESET NOD32 Antivirus, version of virus >>>> signature >>>>> database 6019 (20110406) __________ >>>>> >>>>> The message was checked by ESET NOD32 Antivirus. >>>>> >>>>> http://www.eset.com >>>>> >>>>> _______________________________________________ >>>>> relax (http://nmr-relax.com) >>>>> >>>>> This is the relax-users mailing list >>>>> relax-users@domain.hid >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-users >>>>> >>>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6021 (20110407) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6021 (20110407) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6021 (20110407) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6031 (20110410) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From edward.dauvergne@domain.hid Mon Apr 11 12:41:38 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q9EYk-00035E-Vx for relax-users@domain.hid; 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c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:cc:content-type :content-transfer-encoding; b=BhkSZcR99pScix14OgR72kDOzYCO7nOFEdFp/fouio3S60V+e+1dRrbdz5mXO7YYLU kVSg1de7aensYNkLiOJpXKhIRXHSFIIr+jMT+IaiPPjoxBwIyISxB/eOkw5injUSCcLj Qcupxq1CGZL8CPeFTQ6VnPpFzP/iDLrdEwmoU= MIME-Version: 1.0 Received: by 10.52.99.194 with SMTP id es2mr1341221vdb.216.1302518467988; Mon, 11 Apr 2011 03:41:07 -0700 (PDT) Sender: edward.dauvergne@domain.hid Received: by 10.52.185.130 with HTTP; Mon, 11 Apr 2011 03:41:07 -0700 (PDT) In-Reply-To: <81DC9F5819CB4D7395FEA1359BB2F040@domain.hid> References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid> <78F8FACF15244E5DB30D23776CF896D8@domain.hid> <81DC9F5819CB4D7395FEA1359BB2F040@domain.hid> Date: Mon, 11 Apr 2011 12:41:07 +0200 X-Google-Sender-Auth: Yy1Qk-Gh6iTtxBto2fVijSXeECU Message-ID: Subject: Re: Grid search does not appear to do the job From: "Edward d'Auvergne" To: Tiago Pais Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 11 Apr 2011 10:41:38 -0000 Hi, Would you be able to submit a bug report about this? The link is https://gna.org/bugs/?func=3Dadditem&group=3Drelax. It would be great if you could come up with a script with a tiny, absolutely minimal data set which triggers the bug, and attach these as well. There is definitely a problem, but I am unable to do much with the current info. Actually, one thing to try would be to change "inc=3D[16, 16, 16]" to "inc=3D[1, 16, 16]". Cheers, Edward On 11 April 2011 12:34, Tiago Pais wrote: > Hi Edward, > I have been trying several combinations but the grid search does not appe= ar > to be doing its job. > I have used the following command in the script: > "grid_search(lower=3D[0.111, 0, -0.0], upper=3D[0.111, 1.00, 200], inc=3D= [16, 16, > 16], verbosity=3D7)" > > But I keep seeing this during the calculations: > "Min f: =A0 =A0 =A0 =A0 =A0 =A0 =A03474.82 > > k: 3860 =A0 =A0 xk: [ =A0 =A0 =A0 0.111, =A0 =A00.066667, =A0 =A0 =A0 =A0= =A0-0] fk: nan > > Increment: =A0 =A0 =A0 =A0 =A0array([ 5, 16, 16]) > Params: =A0 =A0 =A0 =A0 =A0 =A0 array([ 0.111, =A01. =A0 , =A0 =A0Inf]) > Min params: =A0 =A0 =A0 =A0 array([ 0.111 =A0 =A0 , =A00.06666667, -0. = =A0 =A0 =A0 =A0]) > f: =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0nan > > Min f: =A0 =A0 =A0 =A0 =A0 =A0 =A03474.82 > > k: 3861 =A0 =A0 xk: [ =A0 =A0 =A0 0.111, =A0 =A00.066667, =A0 =A0 =A0 =A0= =A0-0] fk: nan > > Increment: =A0 =A0 =A0 =A0 =A0array([ 6, 16, 16]) > Params: =A0 =A0 =A0 =A0 =A0 =A0 array([ 0.111, =A01. =A0 , =A0 =A0Inf]) > Min params: =A0 =A0 =A0 =A0 array([ 0.111 =A0 =A0 , =A00.06666667, -0. = =A0 =A0 =A0 =A0]) > f: =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0nan > " > > And at the end the tauS is zero for all spins and the S2s is always close= to > 1. It appears that the space is not being adequately created... > > Any suggestion? > Thanks > Tiago P > > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On > Behalf Of Edward d'Auvergne > Sent: quinta-feira, 7 de Abril de 2011 12:15 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? - SOLVED with 1.3.8 > > Ah, right. =A0I did fix that bug! =A0I thought so :) =A0Ok, if you have a= ny > problems, don't hesitate to ask. > > Bye, > > Edward > > > > On 7 April 2011 13:09, Tiago Pais wrote: >> I have now also running the 1.3.8 version and the problem seems to have >> disappeared. Took me some time to use this version because the column >> numbering has changed, now columns start at number one! Important! ;-) >> >> I hope now this goes well. >> >> Thanks once more for your valuable help. >> Cheers >> Tiago >> >> -----Original Message----- >> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On >> Behalf Of Edward d'Auvergne >> Sent: quinta-feira, 7 de Abril de 2011 10:46 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> I've looked up that line in the specific_fns/model_free/mf_minimise.py >> file, and it looks like you are using an older version of relax. >> Could you copy the output of: >> >> $ relax --info >> >> This looks like an ancient bug that was eliminated a long, long time ago= . >> >> Cheers, >> >> Edward >> >> >> >> >> On 6 April 2011 19:51, Tiago Pais wrote: >>> I used the expression like this: >>> grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], inc=3D[1, = 11, 11]) >>> >>> But I get the following error: >>> Unconstrained grid search size: 121 (constraints may decrease this size= ). >>> >>> Traceback (most recent call last): >>> =A0File "/usr/local/bin/relax", line 418, in >>> =A0 =A0Relax() >>> =A0File "/usr/local/bin/relax", line 127, in __init__ >>> =A0 =A0self.interpreter.run(self.script_file) >>> =A0File "/usr/local/relax/prompt/interpreter.py", line 276, in run >>> =A0 =A0return run_script(intro=3Dself.__intro_string, local=3Dself.loca= l, >>> script_file=3Dscript_file, quit=3Dself.__quit_flag, >>> show_script=3Dself.__show_script, >> raise_relax_error=3Dself.__raise_relax_error) >>> =A0File "/usr/local/relax/prompt/interpreter.py", line 537, in run_scri= pt >>> =A0 =A0return console.interact(intro, local, script_file, quit, >>> show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) >>> =A0File "/usr/local/relax/prompt/interpreter.py", line 433, in >>> interact_script >>> =A0 =A0execfile(script_file, local) >>> =A0File "mf_multimodel_m5S2f0111.py", line 82, in >>> =A0 =A0grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], inc= =3D[1, 11, > 11]) >>> =A0File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_se= arch >>> =A0 =A0minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, >>> constraints=3Dconstraints, verbosity=3Dverbosity) >>> =A0File "/usr/local/relax/generic_fns/minimise.py", line 191, in > grid_search >>> =A0 =A0grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, > constraints=3Dconstraints, >>> verbosity=3Dverbosity) >>> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line > 479, >>> in grid_search >>> =A0 =A0self.minimise(min_algor=3D'grid', lower=3Dlower, upper=3Dupper, = inc=3Dinc, >>> constraints=3Dconstraints, verbosity=3Dverbosity, sim_index=3Dsim_index= ) >>> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line > 922, >>> in minimise >>> =A0 =A0min_options =3D self.grid_search_config(num_params, spin=3Dspin, >>> lower=3Dlower, upper=3Dupper, inc=3Dinc, scaling_matrix=3Dscaling_matri= x) >>> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line > 554, >>> in grid_search_config >>> =A0 =A0self.grid_search_config_fin(min_options, lower, upper, scaling_m= atrix) >>> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line > 631, >>> in grid_search_config_fin >>> =A0 =A0for i in xrange(n): >>> NameError: global name 'n' is not defined >>> >>> >>> Any ideas? >>> >>> Cheers >>> Tiago >>> >>> -----Original Message----- >>> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On >>> Behalf Of Edward d'Auvergne >>> Sent: quarta-feira, 6 de Abril de 2011 18:05 >>> To: Tiago Pais >>> Cc: relax-users@domain.hid >>> Subject: Re: How to set S2f to 0.111? >>> >>> Hi, >>> >>> These match the parameters as listed in the help for the >>> model_free.select_model() user function. =A0The grid search arrays matc= h >>> the parameter arrays. >>> >>> Regards, >>> >>> Edward >>> >>> >>> On 6 April 2011 18:54, Tiago Pais wrote: >>>> Ok, >>>> Im sorry to insist but I am probably missing something here. How do I >>> state >>>> which bound goes with which parameter? That is, which position in the >>> array >>>> bound corresponds to the S2f parameter? >>>> Regards. >>>> TP >>>> >>>> -----Original Message----- >>>> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] O= n >>>> Behalf Of Edward d'Auvergne >>>> Sent: quarta-feira, 6 de Abril de 2011 17:42 >>>> To: Tiago Pais >>>> Cc: relax-users@domain.hid >>>> Subject: Re: How to set S2f to 0.111? >>>> >>>> Hi, >>>> >>>> That is roughly correct. =A0Just set the lower and upper bound to 0.11= 1 >>>> and set the number of increments for that parameter to 1. =A0Then it i= s >>>> like a grid search without S2f being present, or being fixed to 0.111. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 6 April 2011 18:38, Tiago Pais wrote: >>>>> Hi Ed, >>>>> Thanks for the quick reply. >>>>> Let's see if I understand your suggestion. For example, the >>>> mf_multimodel.py >>>>> sample script performs a grid search minimization using the grid_sear= ch >>>>> function. So if I insert an array of upper and lower bounds for the >>>>> parameters in the model I can constrain the interval of possible >> results, >>>>> correct? If so, what is the sequence for the parameters in the array? >>>>> TP >>>>> >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >>>>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>>>> To: Tiago Pais >>>>> Cc: relax-users@domain.hid >>>>> Subject: Re: How to set S2f to 0.111? >>>>> >>>>> Hi, >>>>> >>>>> Unfortunately, there is no ability to fix one of the model-free >>>>> parameters during optimisation in relax yet. =A0This is something tha= t >>>>> has been requested one or two times over the years. =A0This is >>>>> complicated as the gradients and Hessians (first and second partial >>>>> derivates) need to be modified with this in mind, as the curvature of >>>>> the space changes. =A0The fixed parameter is not part of the gradient= or >>>>> Hessian, and has to be removed. =A0This really complicates the target >>>>> function, gradient, and Hessian and, due to the low demand, has not >>>>> been implemented. >>>>> >>>>> Are you able to optimise this parameter and see if you get 0.111? =A0= And >>>>> are you able to extract the timescale of this process (the methyl >>>>> group rotamer jumps)? =A0From memory, someone has optimsed these mode= ls >>>>> using a grid search. =A0This coarse optimisation can be performed in >>>>> relax as you are able to specify the fine details of the grid search. >>>>> It is slower, but will do the job. =A0You could even implement a zoom= ing >>>>> grid search if your scripting skills are up to it to be able to >>>>> relatively quickly find the parameters to high precision. =A0Anyway, = I >>>>> hope this info helps. >>>>> >>>>> Regards, >>>>> >>>>> Edward >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 6 April 2011 17:39, Tiago Pais wrote: >>>>>> Hi, >>>>>> >>>>>> I would like to make an analysis of side-chain relaxation data with > the >>>>> S2f >>>>>> parameter (in model 5) set to 0.111. >>>>>> >>>>>> Is it possible to do this with RELAX? How? >>>>>> >>>>>> Thanks in advance. >>>>>> >>>>>> Cheers >>>>>> >>>>>> Tiago P >>>>>> >>>>>> >>>>>> >>>>>> ************************************** >>>>>> >>>>>> Tiago Pais, PhD. student >>>>>> >>>>>> Cell Physiology & NMR >>>>>> >>>>>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>>>>> >>>>>> >>>>>> >>>>>> __________ Information from ESET NOD32 Antivirus, version of virus >>>>> signature >>>>>> database 6019 (20110406) __________ >>>>>> >>>>>> The message was checked by ESET NOD32 Antivirus. >>>>>> >>>>>> http://www.eset.com >>>>>> >>>>>> _______________________________________________ >>>>>> relax (http://nmr-relax.com) >>>>>> >>>>>> This is the relax-users mailing list >>>>>> relax-users@domain.hid >>>>>> >>>>>> To unsubscribe from this list, get a password >>>>>> reminder, or change your subscription options, >>>>>> visit the list information page at >>>>>> https://mail.gna.org/listinfo/relax-users >>>>>> >>>>>> >>>>> >>>>> __________ Information from ESET NOD32 Antivirus, version of virus >>>> signature >>>>> database 6019 (20110406) __________ >>>>> >>>>> The message was checked by ESET NOD32 Antivirus. >>>>> >>>>> http://www.eset.com >>>>> >>>>> >>>>> >>>>> >>>>> __________ Information from ESET NOD32 Antivirus, version of virus >>>> signature >>>>> database 6019 (20110406) __________ >>>>> >>>>> The message was checked by ESET NOD32 Antivirus. >>>>> >>>>> http://www.eset.com >>>>> >>>>> >>>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6021 (20110407) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6021 (20110407) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6021 (20110407) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signat= ure > database 6031 (20110410) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > From tpais@domain.hid Mon Apr 11 12:50:04 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Q9Egv-0003OB-Fx for relax-users@domain.hid; Mon, 11 Apr 2011 12:50:04 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.3 tests=BAYES_00 autolearn=ham version=3.2.5 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1] helo=mail3.itqb.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1Q9Egv-0003O8-6W for relax-users@domain.hid; Mon, 11 Apr 2011 12:49:57 +0200 Received: from mail3.itqb.unl.pt (localhost.localdomain [127.0.0.1]) by mail3.itqb.unl.pt (Postfix) with ESMTP id C2A14C863B8; Mon, 11 Apr 2011 11:49:56 +0100 (WEST) Received: from Mercurio (mercurio.itqb.unl.pt [193.136.180.146]) by mail3.itqb.unl.pt (Postfix) with ESMTP id 99F0BC86352; Mon, 11 Apr 2011 11:49:56 +0100 (WEST) From: "Tiago Pais" To: "'Edward d'Auvergne'" References: <4BC6F9772C394DE7A4AC86F6AB89F835@domain.hid><78F8FACF15244E5DB30D23776CF896D8@domain.hid><81DC9F5819CB4D7395FEA1359BB2F040@domain.hid> Subject: RE: Grid search does not appear to do the job Date: Mon, 11 Apr 2011 11:50:01 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Mailer: Microsoft Office Outlook 11 Thread-Index: Acv4NPhrQPNoAig9SeuXpxbmYJb9FwAASeeg In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.5994 X-Virus-Scanned: ClamAV using ClamSMTP Cc: relax-users@domain.hid X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 11 Apr 2011 10:50:04 -0000 Ok,=20 I'll do that. (I have tried all possible combinations with the "inc=3D" argument) If you remember I am using version 1.3.8. I tried to install the 1.3.10 because I remember you saying that the grid search here had been = modified but I am getting a "segmentation fault" error when I run this version. Cheers TP -----Original Message----- From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] On Behalf Of Edward d'Auvergne Sent: segunda-feira, 11 de Abril de 2011 11:41 To: Tiago Pais Cc: relax-users@domain.hid Subject: Re: Grid search does not appear to do the job Hi, Would you be able to submit a bug report about this? The link is https://gna.org/bugs/?func=3Dadditem&group=3Drelax. It would be great = if you could come up with a script with a tiny, absolutely minimal data set which triggers the bug, and attach these as well. There is definitely a problem, but I am unable to do much with the current info. Actually, one thing to try would be to change "inc=3D[16, 16, 16]" to "inc=3D[1, 16, 16]". Cheers, Edward On 11 April 2011 12:34, Tiago Pais wrote: > Hi Edward, > I have been trying several combinations but the grid search does not appear > to be doing its job. > I have used the following command in the script: > "grid_search(lower=3D[0.111, 0, -0.0], upper=3D[0.111, 1.00, 200], = inc=3D[16, 16, > 16], verbosity=3D7)" > > But I keep seeing this during the calculations: > "Min f: =A0 =A0 =A0 =A0 =A0 =A0 =A03474.82 > > k: 3860 =A0 =A0 xk: [ =A0 =A0 =A0 0.111, =A0 =A00.066667, =A0 =A0 =A0 = =A0 =A0-0] fk: nan > > Increment: =A0 =A0 =A0 =A0 =A0array([ 5, 16, 16]) > Params: =A0 =A0 =A0 =A0 =A0 =A0 array([ 0.111, =A01. =A0 , =A0 = =A0Inf]) > Min params: =A0 =A0 =A0 =A0 array([ 0.111 =A0 =A0 , =A00.06666667, -0. = =A0 =A0 =A0 =A0]) > f: =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0nan > > Min f: =A0 =A0 =A0 =A0 =A0 =A0 =A03474.82 > > k: 3861 =A0 =A0 xk: [ =A0 =A0 =A0 0.111, =A0 =A00.066667, =A0 =A0 =A0 = =A0 =A0-0] fk: nan > > Increment: =A0 =A0 =A0 =A0 =A0array([ 6, 16, 16]) > Params: =A0 =A0 =A0 =A0 =A0 =A0 array([ 0.111, =A01. =A0 , =A0 = =A0Inf]) > Min params: =A0 =A0 =A0 =A0 array([ 0.111 =A0 =A0 , =A00.06666667, -0. = =A0 =A0 =A0 =A0]) > f: =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0nan > " > > And at the end the tauS is zero for all spins and the S2s is always = close to > 1. It appears that the space is not being adequately created... > > Any suggestion? > Thanks > Tiago P > > > -----Original Message----- > From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On > Behalf Of Edward d'Auvergne > Sent: quinta-feira, 7 de Abril de 2011 12:15 > To: Tiago Pais > Cc: relax-users@domain.hid > Subject: Re: How to set S2f to 0.111? - SOLVED with 1.3.8 > > Ah, right. =A0I did fix that bug! =A0I thought so :) =A0Ok, if you = have any > problems, don't hesitate to ask. > > Bye, > > Edward > > > > On 7 April 2011 13:09, Tiago Pais wrote: >> I have now also running the 1.3.8 version and the problem seems to = have >> disappeared. Took me some time to use this version because the column >> numbering has changed, now columns start at number one! Important! = ;-) >> >> I hope now this goes well. >> >> Thanks once more for your valuable help. >> Cheers >> Tiago >> >> -----Original Message----- >> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On >> Behalf Of Edward d'Auvergne >> Sent: quinta-feira, 7 de Abril de 2011 10:46 >> To: Tiago Pais >> Cc: relax-users@domain.hid >> Subject: Re: How to set S2f to 0.111? >> >> Hi, >> >> I've looked up that line in the = specific_fns/model_free/mf_minimise.py >> file, and it looks like you are using an older version of relax. >> Could you copy the output of: >> >> $ relax --info >> >> This looks like an ancient bug that was eliminated a long, long time = ago. >> >> Cheers, >> >> Edward >> >> >> >> >> On 6 April 2011 19:51, Tiago Pais wrote: >>> I used the expression like this: >>> grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 2, 1E12], = inc=3D[1, 11, 11]) >>> >>> But I get the following error: >>> Unconstrained grid search size: 121 (constraints may decrease this size). >>> >>> Traceback (most recent call last): >>> =A0File "/usr/local/bin/relax", line 418, in >>> =A0 =A0Relax() >>> =A0File "/usr/local/bin/relax", line 127, in __init__ >>> =A0 =A0self.interpreter.run(self.script_file) >>> =A0File "/usr/local/relax/prompt/interpreter.py", line 276, in run >>> =A0 =A0return run_script(intro=3Dself.__intro_string, = local=3Dself.local, >>> script_file=3Dscript_file, quit=3Dself.__quit_flag, >>> show_script=3Dself.__show_script, >> raise_relax_error=3Dself.__raise_relax_error) >>> =A0File "/usr/local/relax/prompt/interpreter.py", line 537, in = run_script >>> =A0 =A0return console.interact(intro, local, script_file, quit, >>> show_script=3Dshow_script, raise_relax_error=3Draise_relax_error) >>> =A0File "/usr/local/relax/prompt/interpreter.py", line 433, in >>> interact_script >>> =A0 =A0execfile(script_file, local) >>> =A0File "mf_multimodel_m5S2f0111.py", line 82, in >>> =A0 =A0grid_search(lower=3D[0.111, 0, 0], upper=3D[0.111, 1, 11], = inc=3D[1, 11, > 11]) >>> =A0File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_search >>> =A0 =A0minimise.grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, >>> constraints=3Dconstraints, verbosity=3Dverbosity) >>> =A0File "/usr/local/relax/generic_fns/minimise.py", line 191, in > grid_search >>> =A0 =A0grid_search(lower=3Dlower, upper=3Dupper, inc=3Dinc, > constraints=3Dconstraints, >>> verbosity=3Dverbosity) >>> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line > 479, >>> in grid_search >>> =A0 =A0self.minimise(min_algor=3D'grid', lower=3Dlower, = upper=3Dupper, inc=3Dinc, >>> constraints=3Dconstraints, verbosity=3Dverbosity, = sim_index=3Dsim_index) >>> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line > 922, >>> in minimise >>> =A0 =A0min_options =3D self.grid_search_config(num_params, = spin=3Dspin, >>> lower=3Dlower, upper=3Dupper, inc=3Dinc, = scaling_matrix=3Dscaling_matrix) >>> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line > 554, >>> in grid_search_config >>> =A0 =A0self.grid_search_config_fin(min_options, lower, upper, scaling_matrix) >>> =A0File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", = line > 631, >>> in grid_search_config_fin >>> =A0 =A0for i in xrange(n): >>> NameError: global name 'n' is not defined >>> >>> >>> Any ideas? >>> >>> Cheers >>> Tiago >>> >>> -----Original Message----- >>> From: edward.dauvergne@domain.hid [mailto:edward.dauvergne@domain.hid] = On >>> Behalf Of Edward d'Auvergne >>> Sent: quarta-feira, 6 de Abril de 2011 18:05 >>> To: Tiago Pais >>> Cc: relax-users@domain.hid >>> Subject: Re: How to set S2f to 0.111? >>> >>> Hi, >>> >>> These match the parameters as listed in the help for the >>> model_free.select_model() user function. =A0The grid search arrays = match >>> the parameter arrays. >>> >>> Regards, >>> >>> Edward >>> >>> >>> On 6 April 2011 18:54, Tiago Pais wrote: >>>> Ok, >>>> Im sorry to insist but I am probably missing something here. How do = I >>> state >>>> which bound goes with which parameter? That is, which position in = the >>> array >>>> bound corresponds to the S2f parameter? >>>> Regards. >>>> TP >>>> >>>> -----Original Message----- >>>> From: edward.dauvergne@domain.hid = [mailto:edward.dauvergne@domain.hid] On >>>> Behalf Of Edward d'Auvergne >>>> Sent: quarta-feira, 6 de Abril de 2011 17:42 >>>> To: Tiago Pais >>>> Cc: relax-users@domain.hid >>>> Subject: Re: How to set S2f to 0.111? >>>> >>>> Hi, >>>> >>>> That is roughly correct. =A0Just set the lower and upper bound to = 0.111 >>>> and set the number of increments for that parameter to 1. =A0Then = it is >>>> like a grid search without S2f being present, or being fixed to = 0.111. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 6 April 2011 18:38, Tiago Pais wrote: >>>>> Hi Ed, >>>>> Thanks for the quick reply. >>>>> Let's see if I understand your suggestion. For example, the >>>> mf_multimodel.py >>>>> sample script performs a grid search minimization using the grid_search >>>>> function. So if I insert an array of upper and lower bounds for = the >>>>> parameters in the model I can constrain the interval of possible >> results, >>>>> correct? If so, what is the sequence for the parameters in the = array? >>>>> TP >>>>> >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: Edward d'Auvergne [mailto:edward.dauvergne@domain.hid] >>>>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>>>> To: Tiago Pais >>>>> Cc: relax-users@domain.hid >>>>> Subject: Re: How to set S2f to 0.111? >>>>> >>>>> Hi, >>>>> >>>>> Unfortunately, there is no ability to fix one of the model-free >>>>> parameters during optimisation in relax yet. =A0This is something = that >>>>> has been requested one or two times over the years. =A0This is >>>>> complicated as the gradients and Hessians (first and second = partial >>>>> derivates) need to be modified with this in mind, as the curvature = of >>>>> the space changes. =A0The fixed parameter is not part of the = gradient or >>>>> Hessian, and has to be removed. =A0This really complicates the = target >>>>> function, gradient, and Hessian and, due to the low demand, has = not >>>>> been implemented. >>>>> >>>>> Are you able to optimise this parameter and see if you get 0.111? = =A0And >>>>> are you able to extract the timescale of this process (the methyl >>>>> group rotamer jumps)? =A0From memory, someone has optimsed these = models >>>>> using a grid search. =A0This coarse optimisation can be performed = in >>>>> relax as you are able to specify the fine details of the grid = search. >>>>> It is slower, but will do the job. =A0You could even implement a = zooming >>>>> grid search if your scripting skills are up to it to be able to >>>>> relatively quickly find the parameters to high precision. = =A0Anyway, I >>>>> hope this info helps. >>>>> >>>>> Regards, >>>>> >>>>> Edward >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 6 April 2011 17:39, Tiago Pais wrote: >>>>>> Hi, >>>>>> >>>>>> I would like to make an analysis of side-chain relaxation data = with > the >>>>> S2f >>>>>> parameter (in model 5) set to 0.111. >>>>>> >>>>>> Is it possible to do this with RELAX? How? >>>>>> >>>>>> Thanks in advance. >>>>>> >>>>>> Cheers >>>>>> >>>>>> Tiago P >>>>>> >>>>>> >>>>>> >>>>>> ************************************** >>>>>> >>>>>> Tiago Pais, PhD. student >>>>>> >>>>>> Cell Physiology & NMR >>>>>> >>>>>> Instituto de Tecnologia Qu=EDmica e Biol=F3gica-Oeiras >>>>>> >>>>>> >>>>>> >>>>>> __________ Information from ESET NOD32 Antivirus, version of = virus >>>>> signature >>>>>> database 6019 (20110406) __________ >>>>>> >>>>>> The message was checked by ESET NOD32 Antivirus. >>>>>> >>>>>> http://www.eset.com >>>>>> >>>>>> _______________________________________________ >>>>>> relax (http://nmr-relax.com) >>>>>> >>>>>> This is the relax-users mailing list >>>>>> relax-users@domain.hid >>>>>> >>>>>> To unsubscribe from this list, get a password >>>>>> reminder, or change your subscription options, >>>>>> visit the list information page at >>>>>> https://mail.gna.org/listinfo/relax-users >>>>>> >>>>>> >>>>> >>>>> __________ Information from ESET NOD32 Antivirus, version of virus >>>> signature >>>>> database 6019 (20110406) __________ >>>>> >>>>> The message was checked by ESET NOD32 Antivirus. >>>>> >>>>> http://www.eset.com >>>>> >>>>> >>>>> >>>>> >>>>> __________ Information from ESET NOD32 Antivirus, version of virus >>>> signature >>>>> database 6019 (20110406) __________ >>>>> >>>>> The message was checked by ESET NOD32 Antivirus. >>>>> >>>>> http://www.eset.com >>>>> >>>>> >>>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>>> >>>> __________ Information from ESET NOD32 Antivirus, version of virus >>> signature >>>> database 6019 (20110406) __________ >>>> >>>> The message was checked by ESET NOD32 Antivirus. >>>> >>>> http://www.eset.com >>>> >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6021 (20110407) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6021 (20110407) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6021 (20110407) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6031 (20110410) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6031 (20110410) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 6031 (20110410) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From zhihongliu.liu@domain.hid Mon Apr 25 10:21:35 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1QEH2s-00040B-JZ for relax-users@domain.hid; Mon, 25 Apr 2011 10:21:35 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-3.6 required=3.3 tests=BAYES_00,HTML_MESSAGE, RCVD_IN_DNSWL_LOW autolearn=ham version=3.2.5 Received: from mail-iy0-f179.google.com ([209.85.210.179]) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1QEH2s-000405-Da for relax-users@domain.hid; Mon, 25 Apr 2011 10:21:26 +0200 Received: by iym7 with SMTP id 7so1807739iym.10 for ; Mon, 25 Apr 2011 01:21:04 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:date:message-id:subject:from:to :content-type; bh=aBAvpC+ASyQHMfWVvOKl1vOWpZcJsvqpikY/ixp+ZBY=; b=InCwV4vYNEAMDYqu89Js/xSkCjLV2KPt4CPY3IsvOGs+c2XgVsvkXUKo1OFiwAH2FU LZJb64y+MdsR1kwlmGPcShysHmVOd2J1Mh9QJsQYTlx8bMCU+28YHQDT33NGjFAMfTzQ cvX4f3dA5IC+lMh/J+N1OQal+RFYzBF7vUwAk= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:date:message-id:subject:from:to:content-type; b=regYu0aIw9kjkg63oujW8Z90z88jnHxWZ/wRfMpKBomSjJLF+nve0pBi7kV2ozV21I 2C3KykaciGvKYlWVHHm0qqT73/nBt5EjjntxkJAQ9Ck4EFyCeayjNRgNwmUZ6uDnbT1a wbEnFH4t+ykXQOkwz7wcSEpicP5GLRbnOYhuY= MIME-Version: 1.0 Received: by 10.42.46.80 with SMTP id j16mr4299350icf.393.1303719663836; Mon, 25 Apr 2011 01:21:03 -0700 (PDT) Received: by 10.42.231.132 with HTTP; Mon, 25 Apr 2011 01:21:03 -0700 (PDT) Date: Mon, 25 Apr 2011 02:21:03 -0600 Message-ID: Subject: Scripts for the N-states model dynamics with PCS and RDCs! From: Zhihong Liu To: relax-users@domain.hid Content-Type: multipart/alternative; boundary=90e6ba614d20731c9a04a1b9e3d4 X-BeenThere: relax-users@domain.hid X-Mailman-Version: 2.1.11 Precedence: list List-Id: "General discussion about the program relax." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 25 Apr 2011 08:21:35 -0000 --90e6ba614d20731c9a04a1b9e3d4 Content-Type: text/plain; charset=ISO-8859-1 Hi, Edward I'm trying to find a proper script in your newest relax release(1.3.10) to calculate the N-states model dynamics. The PCS and RDC data come from the paramagnetic lanthanide ion center. I checked the "sample_scripts" fold and found the only possible one is the "N_state_model.py", which is too short to run any calculation. Can you give me a example to do this kind of calculation? Thanks! best zhihong --90e6ba614d20731c9a04a1b9e3d4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Edward
=A0=A0 I'm trying to find a proper script in your newest = relax release(1.3.10) to calculate the N-states model dynamics. The PCS and= RDC data come from the=A0 paramagnetic lanthanide ion center. I checked th= e "sample_scripts" fold and found the only possible one is the &q= uot;N_state_model.py", which is too short to run any calculation. Can = you give me a example to do this kind of calculation? Thanks!
best
zhihong
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