From aldinoviegas@domain.hid Tue Sep 20 16:23:34 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1R61EL-0005YO-4K for relax-users@domain.hid; Tue, 20 Sep 2011 16:23:34 +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 hermod.pub.dq.fct.unl.pt ([193.136.125.111] helo=hermod.dq.fct.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1R61EL-0005YK-0l for relax-users@domain.hid; Tue, 20 Sep 2011 16:23:25 +0200 Received: from [10.1.94.43] (helo=AldinoPC) by hermod.dq.fct.unl.pt with esmtpa (Exim 4.69) (envelope-from ) id 1R61EI-0006eU-Ae for relax-users@domain.hid; Tue, 20 Sep 2011 15:23:22 +0100 Message-ID: <0AF0ED37C6D14315AA93F647D08FC3AF@AldinoPC> From: "Aldino" To: "Relax" Subject: Model-free - 1 frequency Date: Tue, 20 Sep 2011 15:23:25 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00A0_01CC77A9.3D7073E0" X-Priority: 3 X-MSMail-Priority: Normal Importance: Normal X-Mailer: Microsoft Windows Live Mail 15.4.3538.513 X-MimeOLE: Produced By Microsoft MimeOLE V15.4.3538.513 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: Tue, 20 Sep 2011 14:23:34 -0000 É uma mensagem composta em formato MIME. ------=_NextPart_000_00A0_01CC77A9.3D7073E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, I am using the most recent version of Relax to try to calculate some = dynamic parameters...=20 The thing is that I only have data at one frequency (600 MHz) and when I = try to run the model-free calculation it sais that it need 4 or more = data sets... How can I calculate the model-free parameters with only 3 data sets = (NOE, R1 and R2)? Thank you in advance, Aldino Viegas ______________________________________________ Aldino Viegas, PhD Student Dep. Qu=EDmica, REQUIMTE Faculdade de Ci=EAncias e Tecnologia Universidade Nova de Lisboa 2829-516 Caparica, Portugal Tlf. +351 212948300=20 Ext. 10900 Lab. 106-A=20 aldinoviegas@domain.hid ------=_NextPart_000_00A0_01CC77A9.3D7073E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
I am using the most recent version of Relax to try to calculate = some=20 dynamic parameters...
The thing is that I only have data at one frequency (600 MHz) and = when I=20 try to run the model-free calculation it sais that it need 4 or more = data=20 sets...
How can I=20 calculate the model-free parameters with only 3 data sets (NOE, R1 and=20 R2)?
 
Thank you=20 in advance,
Aldino=20 Viegas
 
 
______________________________________________
Aldino=20 Viegas, PhD Student
Dep. Qu=EDmica, REQUIMTE
Faculdade de = Ci=EAncias e=20 Tecnologia
Universidade Nova de Lisboa
2829-516 Caparica,=20 Portugal

Tlf. +351 212948300
Ext. 10900 Lab. 106-A=20
aldinoviegas@domain.hid ------=_NextPart_000_00A0_01CC77A9.3D7073E0-- From edward.dauvergne@domain.hid Thu Sep 22 10:32:56 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1R6ei8-0004H2-Pl for relax-users@domain.hid; Thu, 22 Sep 2011 10:32:56 +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-vx0-f179.google.com ([209.85.220.179]) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1R6ei8-0004Go-I4 for relax-users@domain.hid; Thu, 22 Sep 2011 10:32:48 +0200 Received: by vcbf1 with SMTP id f1so286462vcb.10 for ; Thu, 22 Sep 2011 01:32:26 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; 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; bh=kpHDVLVucHgLL794kPOTg1YnHfJtyzorlkOfGeT8Vdo=; b=wX3TTh+tz30xOTWissI+DD22SuSee/NuZUCBnxiX+iRdDp2ibhGCXbQvpbS6lppWPk LmmR2OzpJQoDPGIl4DnnTy/p+UzConCNWZBSI/QB+3RAwZIK8wup0qo3WEELyeP8yneG Z2HDONA3xPs6CDtZvBv79KKMV9If/NExJxPd0= MIME-Version: 1.0 Received: by 10.52.173.68 with SMTP id bi4mr1671618vdc.124.1316680346469; Thu, 22 Sep 2011 01:32:26 -0700 (PDT) Sender: edward.dauvergne@domain.hid Received: by 10.52.107.129 with HTTP; Thu, 22 Sep 2011 01:32:26 -0700 (PDT) In-Reply-To: <0AF0ED37C6D14315AA93F647D08FC3AF@AldinoPC> References: <0AF0ED37C6D14315AA93F647D08FC3AF@AldinoPC> Date: Thu, 22 Sep 2011 10:32:26 +0200 X-Google-Sender-Auth: 31gWMqm24iKsrqnkiai4jUI5yrk Message-ID: Subject: Re: Model-free - 1 frequency From: "Edward d'Auvergne" To: Aldino 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, 22 Sep 2011 08:32:57 -0000 Dear Aldino, Welcome to the relax mailing lists. You can for sure use relax to analyse single field strength data, but it is not recommended. relax will do everything Modelfree4 and Dasha will do, plus a lot more. This is not reachable from the GUI though, you will have to implement this in a special script. There are some sample scripts which partly implement this (see the sample_scripts directory), but to put together a full analysis, you will have to do some serious scripting. You have to do this anyway with Modelfree4 or Dasha, as you have to iteratively optimise the diffusion tensor and model-free parameters until convergence (see my paper d'Auvergne and Gooley, 2007 (http://dx.doi.org/10.1039/b702202f) for a review of this procedure, and d'Auvergne and Gooley, 2008b (http://dx.doi.org/10.1007/s10858-007-9213-3) for recent advances). Note that there are many, many issues with using only single field strength data. These are explained in full detail in my review (d'Auvergne and Gooley, 2007). The major problem is that the axial symmetry and rhombicity of the diffusion tensor can be mixed up with chemical exchange and large amplitude ns motions. With single field strength data, the difference between the global diffusion and internal motions can often not be distinguished resulting in either artificial internal Rex and/or ns motions, or the diffusion tensor is incorrect hiding the internal motions of the molecule. Only with multiple field strength data can you distinguish the differences. You sometimes also need to apply the new methodology in d'Auvergne and Gooley, 2008b. This is why you will almost never see a publication with only single field strength data today. Note that using single field strength data, you have to revert to using the state of the art from 1995 (see the Mandel, Akke, and Palmer 1995 paper). Your analysis will be almost two decades behind the current state of the art (some of this is in the links at http://www.nmr-relax.com/refs.html). I hope this information helps. Regards, Edward P. S. This has been asked a number of times before. See https://mail.gna.org/public/relax-users/2008-03/msg00004.html and the links and threads therein for the past discussions. On 20 September 2011 16:23, Aldino wrote: > Dear all, > > I am using the most recent version of Relax to try to calculate some dyna= mic > parameters... > The thing is that I only have data at one frequency (600 MHz) and when I = try > to run the model-free calculation it sais that it need 4 or more data > sets... > How can I calculate the model-free parameters with only 3 data sets (NOE,= R1 > and R2)? > > Thank you in advance, > Aldino Viegas > > > ______________________________________________ > Aldino Viegas, PhD Student > Dep. Qu=EDmica, REQUIMTE > Faculdade de Ci=EAncias e Tecnologia > Universidade Nova de Lisboa > 2829-516 Caparica, Portugal > > Tlf. +351 212948300 > Ext. 10900 Lab. 106-A > aldinoviegas@domain.hid > _______________________________________________ > 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 aldinoviegas@domain.hid Thu Sep 22 11:01:30 2011 Received: from Debian-exim by gna.org with spam-scanned (Exim 4.69) (envelope-from ) id 1R6f9o-0007rX-0A for relax-users@domain.hid; Thu, 22 Sep 2011 11:01:30 +0200 X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on mail.gna.org X-Spam-Level: X-Spam-Status: No, score=-1.0 required=3.3 tests=BAYES_00, RCVD_IN_NJABL_PROXY, STOX_REPLY_TYPE autolearn=no version=3.2.5 Received: from hermod.pub.dq.fct.unl.pt ([193.136.125.111] helo=hermod.dq.fct.unl.pt) by gna.org with esmtp (Exim 4.69) (envelope-from ) id 1R6f9n-0007rU-R5 for relax-users@domain.hid; Thu, 22 Sep 2011 11:01:23 +0200 Received: from a83-132-82-107.cpe.netcabo.pt ([83.132.82.107] helo=NoteBook) by hermod.dq.fct.unl.pt with esmtpa (Exim 4.69) (envelope-from ) id 1R6f9l-0002be-6a; Thu, 22 Sep 2011 10:01:21 +0100 Message-ID: From: "Aldino" To: "Edward d'Auvergne" References: <0AF0ED37C6D14315AA93F647D08FC3AF@AldinoPC> In-Reply-To: Subject: Re: Model-free - 1 frequency Date: Thu, 22 Sep 2011 10:01:12 +0100 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal Importance: Normal X-Mailer: Microsoft Windows Live Mail 15.4.3538.513 X-MimeOLE: Produced By Microsoft MimeOLE V15.4.3538.513 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, 22 Sep 2011 09:01:30 -0000 Dear Edward, thank you for your reply. I really missed this discussion on the mailing list.... The thing is that write now I don't have nor the protein nor the time to acquire data at a different field.... I'll try to work with what I have... Thank you again, Aldino -----Mensagem Original----- From: Edward d'Auvergne Sent: Thursday, September 22, 2011 9:32 AM To: Aldino Cc: relax-users@domain.hid Subject: Re: Model-free - 1 frequency Dear Aldino, Welcome to the relax mailing lists. You can for sure use relax to analyse single field strength data, but it is not recommended. relax will do everything Modelfree4 and Dasha will do, plus a lot more. This is not reachable from the GUI though, you will have to implement this in a special script. There are some sample scripts which partly implement this (see the sample_scripts directory), but to put together a full analysis, you will have to do some serious scripting. You have to do this anyway with Modelfree4 or Dasha, as you have to iteratively optimise the diffusion tensor and model-free parameters until convergence (see my paper d'Auvergne and Gooley, 2007 (http://dx.doi.org/10.1039/b702202f) for a review of this procedure, and d'Auvergne and Gooley, 2008b (http://dx.doi.org/10.1007/s10858-007-9213-3) for recent advances). Note that there are many, many issues with using only single field strength data. These are explained in full detail in my review (d'Auvergne and Gooley, 2007). The major problem is that the axial symmetry and rhombicity of the diffusion tensor can be mixed up with chemical exchange and large amplitude ns motions. With single field strength data, the difference between the global diffusion and internal motions can often not be distinguished resulting in either artificial internal Rex and/or ns motions, or the diffusion tensor is incorrect hiding the internal motions of the molecule. Only with multiple field strength data can you distinguish the differences. You sometimes also need to apply the new methodology in d'Auvergne and Gooley, 2008b. This is why you will almost never see a publication with only single field strength data today. Note that using single field strength data, you have to revert to using the state of the art from 1995 (see the Mandel, Akke, and Palmer 1995 paper). Your analysis will be almost two decades behind the current state of the art (some of this is in the links at http://www.nmr-relax.com/refs.html). I hope this information helps. Regards, Edward P. S. This has been asked a number of times before. See https://mail.gna.org/public/relax-users/2008-03/msg00004.html and the links and threads therein for the past discussions. On 20 September 2011 16:23, Aldino wrote: > Dear all, > > I am using the most recent version of Relax to try to calculate some > dynamic > parameters... > The thing is that I only have data at one frequency (600 MHz) and when I > try > to run the model-free calculation it sais that it need 4 or more data > sets... > How can I calculate the model-free parameters with only 3 data sets (NOE, > R1 > and R2)? > > Thank you in advance, > Aldino Viegas > > > ______________________________________________ > Aldino Viegas, PhD Student > Dep. Química, REQUIMTE > Faculdade de Ciências e Tecnologia > Universidade Nova de Lisboa > 2829-516 Caparica, Portugal > > Tlf. +351 212948300 > Ext. 10900 Lab. 106-A > aldinoviegas@domain.hid > _______________________________________________ > 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 > >