Re: problem loading R1, R2 and nOe files for modelfree -- July 02, 2014 - 09:29

Hi,

For reference, the bug report is at
https://gna.org/bugs/index.php?22257.  I have now fixed the problem in
the relax trunk.  The issue was exactly as I thought, and as I
described in the bug report, but I needed confirmation that this was
indeed the problem as your issue might have been a different bug.  If
you have subversion installed on your system, then you can obtain the
latest code using the command (via a terminal):

svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk

See http://www.nmr-relax.com/download.html#Source_code_repository and
http://www.nmr-relax.com/manual/Latest_sources_relax_repositories.html
for more details.  Otherwise you will have to wait for me to release
relax 3.2.3 with this as well as a few other bug fixes.

Cheers,

Edward



On 1 July 2014 23:29, Ravi Pratap Barnwal <ravi13pb@xxxxxxxxx> wrote:
> Hi Edward,
> I have submitted the bug-report.
>
> regards
> ravi
>
>
> On Mon, Jun 30, 2014 at 12:54 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
> wrote:
> > Hi Ravi,
> >
> > I think I have found what might be causing the problem.  But I'll wait
> > until you have submitted a bug report before making any fixes and
> > releasing a new version of relax, just to be sure that the problem you
> > are seeing is the problem I am fixing.
> >
> > Cheers,
> >
> > Edward
> >
> >
> > On 30 June 2014 08:28, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > > Hi Ravi,
> > >
> > > I'm having difficulty replicating the issue.  Would you be able to
> > > create a bug report using the link
> > > https://gna.org/bugs/?func=additem&group=relax ?  Cheers!  The more
> > > information you include the better.  For example the minimal steps
> > > require to trigger the bug.  You could also attach your screenshot
> > > there.  If there is enough detail for me to replicate the bug, then it
> > > usually takes me 5-10 minutes to fix it.  I could then release relax
> > > 3.2.3 later this week with the fix.
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > > On 27 June 2014 21:04, Ravi Pratap Barnwal <ravi13pb@xxxxxxxxx> wrote:
> > > > Hi Edward,
> > > > I am using version 3.2.2 on mac 10.8.5 (mountain lion). I am using GUI
> > > > mode
> > > > to run the relax. Here is the report from "Tools-> System Information"
> > > >
> > > >
> > > >
> > > >
> > > >                                             relax 3.2.2
> > > >
> > > >                               Molecular dynamics by NMR data analysis
> > > >
> > > >                              Copyright (C) 2001-2006 Edward d'Auvergne
> > > >                          Copyright (C) 2006-2014 the relax development
> > > > team
> > > >
> > > > This is free software which you are welcome to modify and redistribute
> > > > under
> > > > the conditions of the
> > > > GNU General Public License (GPL).  This program, including all modules,
> > > > is
> > > > licensed under the GPL
> > > > and comes with absolutely no warranty.  For details type 'GPL' within
> > > > the
> > > > relax prompt.
> > > >
> > > > Assistance in using the relax prompt and scripting interface can be
> > > > accessed
> > > > by typing 'help' within
> > > > the prompt.
> > > >
> > > > Processor fabric:  Uni-processor.
> > > >
> > > >
> > > > relax> sys_info()
> > > >
> > > > Hardware information:
> > > >     Machine:                 x86_64
> > > >     Processor:               i386
> > > >     Processor name:          Intel(R) Xeon(R) CPU           W3530  @
> > > > 2.80GHz
> > > >     Endianness:              little
> > > >     Total RAM size:          2048.0 Mb
> > > >     Total swap size:         11264.0 Mb
> > > >
> > > > Operating system information:
> > > >     System:                  Darwin
> > > >     Release:                 12.5.0
> > > >     Version:                 Darwin Kernel Version 12.5.0: Sun Sep 29
> > > > 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64
> > > >     Mac version:             10.8.5 (, , ) x86_64
> > > >     Distribution:
> > > >     Full platform string:    Darwin-12.5.0-x86_64-i386-64bit
> > > >
> > > > Python information:
> > > >     Architecture:            64bit
> > > >     Python version:          2.7.2
> > > >     Python branch:
> > > >     Python build:            default, Apr  5 2012 18:46:15
> > > >     Python compiler:         GCC 4.2.1 (Apple Inc. build 5666) (dot 3)
> > > >     Libc version:
> > > >     Python implementation:   CPython
> > > >     Python revision:
> > > >     Python executable:
> > > > /Applications/relax.app/Contents/MacOS/python
> > > >     Python flags:            sys.flags(debug=0, py3k_warning=0,
> > > > division_warning=0, division_new=0, inspect=0, interactive=0,
> > > > optimize=1,
> > > > dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
> > > > tabcheck=0, verbose=0, unicode=0, bytes_warning=0)
> > > >     Python float info:
> > > > sys.float_info(max=1.7976931348623157e+308,
> > > > max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308,
> > > > min_exp=-1021,
> > > > min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
> > > > radix=2, rounds=1)
> > > >     Python module path:
> > > > ['/Applications/relax.app/Contents/Resources/lib/python27.zip',
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7',
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-darwin',
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-mac',
> > > >
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-mac/lib-scriptpackages',
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/lib-tk',
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/lib-old',
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/lib-dynload',
> > > >
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip',
> > > >
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/site-packages',
> > > >
> > > > '/Applications/relax.app/Contents/Resources/lib/python2.7/site-packages']
> > > >
> > > > Python packages and modules (most are optional):
> > > >
> > > > Name               Installed    Version                        Path
> > > > minfx              True         1.0.6
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/minfx
> > > > bmrblib            True         1.0.3
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/bmrblib
> > > > numpy              True         1.6.1
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/numpy
> > > > scipy              True         0.10.1
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/scipy
> > > > wxPython           True         2.9.3.1 osx-cocoa (classic)
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/wx
> > > > matplotlib         False
> > > > mpi4py             True         1.2.2
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/mpi4py
> > > > epydoc             True         3.0.1
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/epydoc
> > > > optparse           True         1.5.3
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/optparse.pyc
> > > > readline           False
> > > > profile            True
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/profile.pyc
> > > > bz2                True
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/lib-dynload/bz2.so
> > > > gzip               True
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/gzip.pyc
> > > > io                 True
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/io.pyc
> > > > xml                True         0.8.4 (internal)
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/xml/__init__.pyc
> > > > xml.dom.minidom    True
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/xml/dom/minidom.pyc
> > > >
> > > > relax information:
> > > >     Version:                 3.2.2
> > > >     Processor fabric:        Uni-processor.
> > > >
> > > > relax C modules:
> > > >
> > > > Module                        Compiled    File type
> > > > Path
> > > > target_functions.relax_fit    True        3-way bundle (i386, ppc,
> > > > x86_64)
> > > >
> > > > /Applications/relax.app/Contents/Resources/lib/python2.7/lib-dynload/target_functions/relax_fit.so
> > > >
> > > >
> > > >
> > > > regards
> > > > ravi
> > > >
> > > >
> > > > On Fri, Jun 27, 2014 at 12:28 AM, Edward d'Auvergne
> > > > <edward@xxxxxxxxxxxxx>
> > > > wrote:
> > > > > Hi Ravi,
> > > > >
> > > > > Which version of relax are you using and which operating system are
> > > > > you running it on?  Are you using the newest 3.2.2 version?  Could you
> > > > > run 'relax -i' or, in the GUI, select the 'Tools->System information'
> > > > > menu item and the copy and paste the output into the body of a new
> > > > > email?  Note that due to too much abuse of the system, attachments are
> > > > > no longer allowed on the relax mailing lists to avoid excessive strain
> > > > > on the open source infrastructure.  All attachments are filtered, i.e.
> > > > > stripped from the message.  See your archived message at
> > > > > http://article.gmane.org/gmane.science.nmr.relax.user/1695 for
> > > > > example.  If you would like to share a file in such a situation, the
> > > > > best solution is to create a bug report using the link
> > > > > https://gna.org/bugs/?func=additem&group=relax and to attach the file
> > > > > there.  There are also support requests for non-bug related issues
> > > > > where files can also be attached
> > > > > (https://gna.org/support/?func=additem&group=relax).
> > > > >
> > > > > Cheers,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > > On 27 June 2014 00:50, Ravi Pratap Barnwal <ravi13pb@xxxxxxxxx> wrote:
> > > > > > Hi,
> > > > > > I am encountering problem while loading R1,R2 and nOe values
> > > > > > calculated
> > > > > > for
> > > > > > two different fields into relax (precompiled version 3.2.2) for mac
> > > > > > 10.8.5.
> > > > > > When i try to add the data and try to change the "free format file
> > > > > > settings" for respective file, it is kind of hanging and does not
> > > > > > proceed
> > > > > > anywhere. My files are in the following format,
> > > > > > 3       GLY     1.814795542     0.090739777
> > > > > > 4       SER     2.267446596     0.11337233
> > > > > > 5       MET     2.621469801     0.13107349
> > > > > > 6       ASP     2.751590887     0.137579544
> > > > > >
> > > > > >
> > > > > > Am i doing something wrong? I am following the protocol from this
> > > > > > link,
> > > > > >
> > > > > >
> > > > > >
> > > > > > http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_data_pipe_initialisation.html
> > > > > >
> > > > > > I have attached a screen-shot for the problem. Any help is highly
> > > > > > appreciated.
> > > > > >
> > > > > > regards
> > > > > > ravi
> > > > > > _______________________________________________
> > > > > > relax (http://www.nmr-relax.com)
> > > > > >
> > > > > > This is the relax-users mailing list
> > > > > > relax-users@xxxxxxx
> > > > > >
> > > > > > 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
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > --With best wishes
> > > > Ravi Pratap Barnwal, Ph. D.
> > > > Research Associate,
> > > > Prof. G Varani's Group,
> > > > Department of Chemistry,
> > > > University of Washington, Seattle
> > > > WA 98195-1700
> > > > USA
> > > > Phone-206 617 9423 (M)
> > > > Email- barnwal@xxxxxxxxxxxxxxxx
>
>
>
>
> --
> --With best wishes
> Ravi Pratap Barnwal, Ph. D.
> Research Associate,
> Prof. G Varani's Group,
> Department of Chemistry,
> University of Washington, Seattle
> WA 98195-1700
> USA
> Phone-206 617 9423 (M)
> Email- barnwal@xxxxxxxxxxxxxxxx