Hi,
I've just tested out the script and peak height file, and all seems to
be ok. All of the intensities have been read into relax. There are 3
that are skipped though. One of these NMRView lines looks like:
18 {} 9.27778 0.02133 0.02569 ++ {0.0} {} {} 118.21079 0.19138 0.23045
++ {0.0} {} 1.56790685654 0.4263 -1 {} 0
whereas a normal line looks like:
17 {68.HN} 9.25599 0.03338 0.02959 ++ {0.0} {} {68.N} 118.91410
0.19320 0.16381 ++ {0.0} {} 1.11185908318 0.2807 0 {} 0
The problem with line 18 is that the peak is unlabelled. From line
17, relax is taking the residue number 68 from '{68.HN}' and
heteronucleus and proton names as 'HN' and 'N'. But in line 18, the
residue info is missing, so this line is ignored. Are there other
problems other than these relax warnings?
Cheers,
Edward
On 9 March 2011 15:35, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/bugs/?17876>
Summary: relax_fit script failing
Project: relax
Submitted by: None
Submitted on: Wed 09 Mar 2011 02:35:45 PM UTC
Category: relax sample scripts
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name: Elio
Originator Email: herfworm@xxxxxxxxx
Open/Closed: Open
Discussion Lock: Any
Release: 1.3.10
Operating System: GNU/Linux
_______________________________________________________
Details:
Hi Edward. Hopefully these will help diagnosing the problem I am having. It
is probably something simple I am missing when using the new sample scrips
with 1.3.10 since things were running fine with 1.3.3 and the old script.
The
test suite passed and the output of relax --info is below and other
requested
files are attached. Thanks for your help.
relax 1.3.10
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2011 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.
Hardware information:
Machine: x86_64
Processor: x86_64
System information:
System: Linux
Release: 2.6.18-8.1.8.el5
Version: #1 SMP Tue Jul 10 06:39:17 EDT 2007
GNU/Linux version: CentOS 5.5 Final
Distribution: redhat 5.5 Final
Full platform string:
Linux-2.6.18-8.1.8.el5-x86_64-with-redhat-5.5-Final
Software information:
Architecture: 64bit ELF
Python version: 2.7.1
Python branch: tags/r271
Python build: r271:86832, Mar 8 2011 14:55:08
Python compiler: GCC 4.1.2 20080704 (Red Hat 4.1.2-48)
Python implementation: CPython
Python revision: 86832
Numpy version: 1.5.1
Libc version: glibc 2.3
Python packages (most are optional):
Package Installed Version Path
minfx True Unknown /usr/local/relax/minfx
bmrblib False
numpy True 1.5.1
/usr/local/lib/python2.7/site-packages/numpy
ScientificPython False
wxPython False
mpi4py False
epydoc False
optparse True 1.5.3
/usr/local/lib/python2.7/optparse.pyc
Numeric False
readline True
/usr/local/lib/python2.7/lib-dynload/readline.so
profile True
/usr/local/lib/python2.7/profile.pyc
bz2 True
/usr/local/lib/python2.7/lib-dynload/bz2.so
gzip True
/usr/local/lib/python2.7/gzip.pyc
os.devnull True
/usr/local/lib/python2.7/os.pyc
Compiled relax C modules:
Relaxation curve fitting: True
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Wed 09 Mar 2011 02:35:45 PM UTC Name: 1ubq.pdb Size: 59kB By: None
<http://gna.org/bugs/download.php?file_id=12643>
-------------------------------------------------------
Date: Wed 09 Mar 2011 02:35:45 PM UTC Name: 500.xpk Size: 9kB By: None
<http://gna.org/bugs/download.php?file_id=12644>
-------------------------------------------------------
Date: Wed 09 Mar 2011 02:35:45 PM UTC Name: relax_fit.py Size: 4kB By:
None
<http://gna.org/bugs/download.php?file_id=12645>
-------------------------------------------------------
Date: Wed 09 Mar 2011 02:35:45 PM UTC Name: output Size: 14kB By: None
<http://gna.org/bugs/download.php?file_id=12646>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?17876>
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Re: [bug #17876] relax_fit script failing