URL:
http://gna.org/bugs/?7596
Summary: Error using pdb.create_tensor_pdb() on amd64 Linux
Project: relax
Submitted by: None
Submitted on: Wednesday 11/01/2006 at 03:28 CET
Category: None
Priority: 5 -
.
___
Follow-up Comments:
---
Date: Wednesday 11/08/2006 at 13:52 CETBy: Anonymous
I'm using the tensor_pdb version (svn co
svn://svn.gna.org/svn/relax/branches/tensor_pdb) and running Mac OS X 10.4.8
w/ gcc version 4.0.1 (PowerPC
URL:
http://gna.org/bugs/?8996
Summary: Bugs in palmer.py
Project: relax
Submitted by: None
Submitted on: Wednesday 04/25/2007 at 12:32 CEST
Category: relax's source code
Severity: 3 - Normal
URL:
http://gna.org/bugs/?8997
Summary: bug in palmer.py stage 2
Project: relax
Submitted by: None
Submitted on: Wednesday 04/25/2007 at 12:36 CEST
Category: relax's source code
Severity: 3 - Normal
URL:
http://gna.org/bugs/?9188
Summary: Residue selection in full_analysis.py
Project: relax
Submitted by: None
Submitted on: Wednesday 05/23/2007 at 14:15 CEST
Category: None
Severity: 2 - Minor
URL:
http://gna.org/bugs/?9189
Summary: Undefined functions in mf.py
Project: relax
Submitted by: None
Submitted on: Wednesday 05/23/2007 at 14:18 CEST
Category: None
Severity: 3 - Normal
URL:
http://gna.org/bugs/?9238
Summary: Error in setting the heteronuclear frequency in
'maths_fns/jw_mapping.py'
Project: relax
Submitted by: None
Submitted on: Wednesday 05/30/2007 at 02:10 CEST
Category: relax's
URL:
http://gna.org/bugs/?9259
Summary: Reduced spectral density mapping yielding bad
values
Project: relax
Submitted by: None
Submitted on: Friday 06/01/2007 at 17:15 CEST
Category: relax's source code
Additional Item Attachment, bug #9188 (project relax):
File name: results.bz2Size:6 KB
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URL:
http://gna.org/bugs/?9892
Summary: CONV_LOOP error
Project: relax
Submitted by: None
Submitted on: Wednesday 08/29/2007 at 19:33 CEST
Category: relax's source code
Severity: 4 - Important
URL:
http://gna.org/bugs/?10189
Summary: latex_mf_table.py: undefined variable
Project: relax
Submitted by: None
Submitted on: Tuesday 10/23/2007 at 20:58 CEST
Category: relax's source code
Severity: 2 -
URL:
http://gna.org/bugs/?10320
Summary: bug in model-free.py; All residues must either have
a local tm parameter or not
Project: relax
Submitted by: None
Submitted on: Tuesday 11/13/2007 at 17:57 CET
Category: relax's
URL:
http://gna.org/bugs/?10323
Summary: jw_mapping.py: Element instance has no attribute
'num_ri'
Project: relax
Submitted by: None
Submitted on: Tuesday 11/13/2007 at 21:52 CET
Category: relax's source code
URL:
http://gna.org/bugs/?11383
Summary: calling relax_data.display fails
Project: relax
Submitted by: None
Submitted on: Thursday 03/27/2008 at 17:32 CET
Category: relax's source code
Severity: 3 -
URL:
http://gna.org/bugs/?12607
Summary: RelaxError: Grid search size too large
Project: relax
Submitted by: None
Submitted on: Tuesday 11/18/2008 at 00:28 CET
Category: relax's source code
Severity: 3 -
URL:
http://gna.org/bugs/?13259
Summary: full analysis-high Te values
Project: relax
Submitted by: None
Submitted on: Wednesday 03/25/2009 at 21:01 CET
Category: relax's source code
Severity: 3 - Normal
Follow-up Comment #2, sr #2336 (project relax):
Would it be possible to post a basic protocol explaining how to get relax to
expect a xpk list instead of sparky? You say that the relax_fit.py script
has an example of howe to use spectrum.read_intensities(), however, that
function is not listed
Follow-up Comment #3, sr #2336 (project relax):
I am using 1.3.3. I still have no clue how to get it to expect nmrview
opposed to sparky.
___
Reply to this item at:
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Follow-up Comment #4, sr #2336 (project relax):
Thanks for the help. It now works! However, I am having trouble with the
error values. The SDev for the noise in the spectra from nmrview is 0.0.
However, if I use the RMSD function in sparky to get noise values, the errors
on the plotted figures
Follow-up Comment #7, sr #2336 (project relax):
I am processing some T1, T1rho, and NOE data using 1.3.3. The process
completes, however, the resulting grace plots show very high error values
(150% for some residues). I am only using strong, well-defined peaks, and I
know the data is of fairly
Follow-up Comment #9, sr #2336 (project relax):
The plotted Rx vales have the large errors. I am just using the relax_fit.py
script for T1 and T1rho. The fitting is the default (exp).
___
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Follow-up Comment #12, sr #2336 (project relax):
hanks for the reply.
1) Which program are you using to measure peak intensities?
nmrviewj
2) For peak intensities, are you using heights or volumes?
intensities from nmrviewj
3) How exactly are you getting your noise estimates?
RMSD
URL:
http://gna.org/bugs/?13744
Summary: relax fails to report convergence even though
output files are identical
Project: relax
Submitted by: None
Submitted on: Monday 06/22/2009 at 20:20 CEST
Category: relax's source
URL:
http://gna.org/support/?2402
Summary: high SSE values with Model Free runs
Project: relax
Submitted by: None
Submitted on: Tuesday 08/04/2009 at 16:47 CEST
Category: None
Priority: 5 - Normal
URL:
http://gna.org/bugs/?14428
Summary: palmer.py problem wihen spins have no data
Project: relax
Submitted by: None
Submitted on: Friday 10/02/2009 at 20:04 CEST
Category: relax's source code
Severity:
URL:
http://gna.org/bugs/?14941
Summary: Final Run error message
Project: relax
Submitted by: None
Submitted on: Monday 12/14/2009 at 16:57 CET
Category: None
Severity: 3 - Normal
Additional Item Attachment, bug #14941 (project relax):
File name: full_analysis_test.py Size:29 KB
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Follow-up Comment #4, bug #14941 (project relax):
I did the update using svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3
command but I still get a similar traceback...
Thank you for working on this!
Traceback (most recent call last):
File /usr/local/bin/relax, line 418, in ?
Relax()
URL:
http://gna.org/support/?2470
Summary: main relax python script fails to start, python
2.6.2 (Ubuntu Jaunty kernel 2.6.28-17)
Project: relax
Submitted by: None
Submitted on: Thursday 12/17/09 at 12:56 CET
Category:
URL:
http://gna.org/bugs/?15148
Summary: Modsel.py crashes with multiple spin data
Project: relax
Submitted by: None
Submitted on: Monday 01/18/2010 at 15:03 CET
Category: None
Severity: 5 - Blocker
URL:
http://gna.org/bugs/?17276
Summary: After submitting the lists into Relax the following
error is found 'list index is out of range'
Project: relax
Submitted by: None
Submitted on: Wed 08 Dec 2010 06:04:27 PM UTC
URL:
http://gna.org/bugs/?17343
Summary: CH2 atom is missing
Project: relax
Submitted by: None
Submitted on: Fri 17 Dec 2010 06:51:39 PM UTC
Category: relax's source code
Severity: 2 - Minor
URL:
http://gna.org/bugs/?17458
Summary: Prolate tensor converging to oblate
Project: relax
Submitted by: None
Submitted on: Mon 10 Jan 2011 05:00:58 PM UTC
Category: relax's source code
Severity: 4 -
URL:
http://gna.org/bugs/?17476
Summary: Missing data points triggers failure of R1 or R2.py
script
Project: relax
Submitted by: None
Submitted on: Thu 13 Jan 2011 12:20:59 PM UTC
Category: relax's source code
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
URL:
http://gna.org/bugs/?18554
Summary: dauvergne protocol sample script
Project: relax
Submitted by: None
Submitted on: Wed 24 Aug 2011 12:36:22 PM UTC
Category: relax sample scripts
Severity: 3 -
URL:
http://gna.org/bugs/?18789
Summary: no error values using relax_fit.py with
non-duplicated spectra
Project: relax
Submitted by: None
Submitted on: Wed 05 Oct 2011 03:07:16 PM UTC
Category: None
URL:
http://gna.org/bugs/?18790
Summary: UnboundLocalError: local variable 'spin_id'
referenced before assignment
Project: relax
Submitted by: None
Submitted on: Wed 05 Oct 2011 04:07:25 PM UTC
Category: relax's source
Follow-up Comment #7, bug #18789 (project relax):
Great Edward! So was this in fact a bug? If so, how do I go about getting the
fix? Thanks.
___
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URL:
http://gna.org/bugs/?18807
Summary: Diffusion tensor not initializing with ave=False
Project: relax
Submitted by: None
Submitted on: Tue 11 Oct 2011 07:52:06 PM UTC
Category: relax's source code
URL:
http://gna.org/bugs/?19323
Summary: Diffusion tensor orientation
Project: relax
Submitted by: None
Submitted on: Mon 23 Jan 2012 08:06:24 PM UTC
Category: relax's source code
Severity: 4 - Important
URL:
http://gna.org/bugs/?19528
Summary: MemoryError during final run of d'Auvergne
Protocol
Project: relax
Submitted by: None
Submitted on: Tue Mar 6 11:25:33 2012
Category: relax's source code
Severity:
URL:
http://gna.org/bugs/?19606
Summary: GUI app launcher crashes
Project: relax
Submitted by: None
Submitted on: Mon 02 Apr 2012 08:13:10 AM UTC
Category: GUI
Severity: 3 - Normal
Additional Item Attachment, task #7581 (project relax):
File name: relax-py.info Size:2 KB
File name: relax-py.patch Size:2 KB
___
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URL:
http://gna.org/bugs/?19887
Summary: Execution of relax_fit.py and the relaxation curve
fitting failed
Project: relax
Submitted by: None
Submitted on: Mon 02 Jul 2012 08:27:01 AM UTC
Category: relax sample scripts
URL:
http://gna.org/bugs/?19987
Summary: GUI opens and closes immediately
Project: relax
Submitted by: None
Submitted on: Fri 27 Jul 2012 03:09:18 PM UTC
Category: GUI
Severity: 3 - Normal
URL:
http://gna.org/bugs/?20132
Summary: Bugs
Project: relax
Submitted by: None
Submitted on: Tue 04 Sep 2012 02:01:51 PM UTC
Category: GUI
Severity: 3 - Normal
Priority: 5 - Normal
URL:
http://gna.org/bugs/?20133
Summary: Bug 2
Project: relax
Submitted by: None
Submitted on: Tue 04 Sep 2012 02:22:33 PM UTC
Category: GUI
Severity: 3 - Normal
Priority: 5 - Normal
URL:
http://gna.org/bugs/?20136
Summary: bug NOE
Project: relax
Submitted by: None
Submitted on: Tue 04 Sep 2012 03:20:36 PM UTC
Category: GUI
Severity: 3 - Normal
Priority: 5 - Normal
URL:
http://gna.org/bugs/?20152
Summary: Import T1 demo.txt from DC to Relax
Project: relax
Submitted by: None
Submitted on: Thu 06 Sep 2012 09:00:04 PM UTC
Category: GUI
Severity: 3 - Normal
URL:
http://gna.org/bugs/?20174
Summary: run mf_multimodel.py in relax
Project: relax
Submitted by: None
Submitted on: Mon 17 Sep 2012 04:30:17 PM UTC
Category: relax sample scripts
Severity: 3 - Normal
URL:
http://gna.org/bugs/?20175
Summary: run mf_multimodel.py in relax (cmd)
Project: relax
Submitted by: None
Submitted on: Tue 18 Sep 2012 10:34:40 AM UTC
Category: relax sample scripts
Severity: 3 -
URL:
http://gna.org/bugs/?20176
Summary: run mf_multimodel.py in relax (cmd)
Project: relax
Submitted by: None
Submitted on: Tue 18 Sep 2012 10:41:59 AM UTC
Category: relax sample scripts
Severity: 3 -
URL:
http://gna.org/bugs/?20201
Summary: run mf_multimodel.py in relax (cmd)
Project: relax
Submitted by: None
Submitted on: Wed 26 Sep 2012 05:21:38 PM UTC
Category: relax sample scripts
Severity: 3 -
URL:
http://gna.org/bugs/?20203
Summary: run palmer.py in relax
Project: relax
Submitted by: None
Submitted on: Fri 28 Sep 2012 10:23:35 AM UTC
Category: relax sample scripts
Severity: 3 - Normal
URL:
http://gna.org/bugs/?20277
Summary: RelaxError: The data pipe 'aic - mf' has not been
created yet.
Project: relax
Submitted by: None
Submitted on: Wed 31 Oct 2012 03:27:08 PM UTC
Category: GUI
URL:
http://gna.org/support/?2999
Summary: Import BMRB data to Relax
Project: relax
Submitted by: None
Submitted on: Mon 14 Jan 2013 03:19:03 PM UTC
Category: None
Priority: 5 - Normal
URL:
http://gna.org/support/?3000
Summary: Import BMRB data to Relax
Project: relax
Submitted by: None
Submitted on: Mon 14 Jan 2013 05:13:13 PM UTC
Category: None
Priority: 5 - Normal
Follow-up Comment #1, sr #2998 (project relax):
Hi Edward,
I am sorry about that, attached please find the BMRB and pdb files.
http://thread.gmane.org/gmane.science.nmr.relax.user/1381
Regards,
Mengjun
(file #16943, file #16944, file #16945, file #16946)
Follow-up Comment #8, sr #2998 (project relax):
Hi Edward,
I have tried the new relax version 2.2.1 to load the BMRB data again, this
time the relax error come up:
RelaxError: Multiple alternate location indicators are present in the PDB
file, but the desired coordinate set has not been
URL:
http://gna.org/support/?3017
Summary: relaxerror in dauvergne_protocol.py
Project: relax
Submitted by: None
Submitted on: Thu 28 Mar 2013 12:47:01 PM UTC
Category: None
Priority: 5 - Normal
URL:
http://gna.org/bugs/?20674
Summary: UnboundLocalError in consistency_tests.py
Project: relax
Submitted by: None
Submitted on: Thu 28 Mar 2013 03:37:52 PM UTC
Category: relax sample scripts
Severity: 3
Additional Item Attachment, bug #20674 (project relax):
File name: T1 dhp 700.txt Size:74 KB
File name: T2 dhp 500.txt Size:67 KB
File name: T2 dhp 700.txt Size:68 KB
File name: logconsistency Size:371 KB
Additional Item Attachment, bug #20674 (project relax):
File name: 2QFK_MONOMERHabc5.pdb Size:282 KB
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URL:
http://gna.org/bugs/?20683
Summary: relaxerror in dauvergne_protocol.py
Project: relax
Submitted by: None
Submitted on: Fri 29 Mar 2013 05:07:38 PM UTC
Category: relax sample scripts
Severity: 3 -
Additional Item Attachment, bug #20683 (project relax):
File name: NOE dhp 500.txtSize:25 KB
File name: NOE dhp 700.txtSize:25 KB
File name: T2 dhp 500.txt Size:67 KB
File name: T2 dhp 700.txt Size:68 KB
Additional Item Attachment, bug #20683 (project relax):
File name: log dauvergne_protocol Size:704 KB
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URL:
http://gna.org/bugs/?20934
Summary: modelfree calculation halts with the following
exception
Project: relax
Submitted by: None
Submitted on: Fri Jun 28 13:39:04 2013
Category: relax sample scripts
URL:
http://gna.org/bugs/?21001
Summary: crash for multi-processor grid search using 'sphere'
model
Project: relax
Submitted by: None
Submitted on: Thu 01 Aug 2013 08:16:04 PM UTC
Category: relax sample scripts
Additional Item Attachment, bug #21001 (project relax):
File name: noe.500.outSize:0 KB
File name: logSize:57 KB
___
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Additional Item Attachment, bug #21079 (project relax):
File name: local_tm.rar Size:966 KB
___
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Additional Item Attachment, bug #21079 (project relax):
File name: results_data.rar Size:326 KB
___
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URL:
http://gna.org/bugs/?21338
Summary: Some png have invalid profiles embedded
Project: relax
Submitted by: None
Submitted on: Wed 11 Dec 2013 05:21:08 PM UTC
Category: relax's source code
Severity: 3 -
Additional Item Attachment, bug #21338 (project relax):
File name: nessy.png-48x48Size:3 KB
File name: nessy.png-128x128 Size:20 KB
File name: nessy.png-wizard Size:41 KB
File name: bruker.png-48x48 Size:1 KB
Additional Item Attachment, bug #21338 (project relax):
File name: bruker.png-128x128 Size:4 KB
File name: bruker.png-wizard Size:5 KB
___
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URL:
http://gna.org/bugs/?21615
Summary: Model-free analysis error (7 Feb 2014)
Project: relax
Submitted by: None
Submitted on: Fri 07 Feb 2014 09:07:58 PM UTC
Category: GUI
Specific analysis category: Model-free analysis
URL:
http://gna.org/bugs/?21695
Summary: Full test suite
Project: relax
Submitted by: None
Submitted on: Wed 19 Feb 2014 10:58:22 PM UTC
Category: Test suite
Specific analysis category: None
Priority: 5 -
Follow-up Comment #2, bug #21695 (project relax):
Hi Edward,
Thank you so much for your suggestion. I have get the output by accessing via
the Tools-System information menu
entry in the GUI, please see the attached file.
Regards,
Mengjun
(file #20128)
URL:
http://gna.org/bugs/?21754
Summary: qtgrace
Project: relax
Submitted by: None
Submitted on: Tue 04 Mar 2014 07:55:34 PM UTC
Category: GUI
Specific analysis category: Relaxation curve-fitting
Priority:
URL:
http://gna.org/bugs/?21813
Summary: file recognition
Project: relax
Submitted by: None
Submitted on: Tue 18 Mar 2014 09:22:33 AM UTC
Category: None
Specific analysis category: Model-free analysis
URL:
http://gna.org/bugs/?21814
Summary: PDB file format
Project: relax
Submitted by: None
Submitted on: Tue 18 Mar 2014 05:36:02 PM UTC
Category: None
Specific analysis category: Model-free analysis
URL:
http://gna.org/bugs/?21862
Summary: Programme freezes up
Project: relax
Submitted by: None
Submitted on: Tue 25 Mar 2014 15:30:47 UTC
Category: GUI
Specific analysis category: Model-free analysis
Additional Item Attachment, bug #21862 (project relax):
File name: Ubiquitin2.bz2 Size:277 KB
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URL:
http://gna.org/support/?3142
Summary: Error messages Relax-3.1.7
Project: relax
Submitted by: None
Submitted on: Thu 03 Apr 2014 07:30:07 PM UTC
Category: Feature request
Priority: 5 - Normal
URL:
http://gna.org/bugs/?21959
Summary: cpmg_analysis
Project: relax
Submitted by: None
Submitted on: Wed 23 Apr 2014 09:43:15 AM UTC
Category: relax sample scripts
Specific analysis category: None
URL:
http://gna.org/bugs/?22039
Summary: Dpar value printed twice in the diffusion tensor
display
Project: relax
Submitted by: None
Submitted on: Wed 14 May 2014 03:57:42 PM UTC
Category: relax's source code
Specific
URL:
http://gna.org/bugs/?22131
Summary: can not quit after I modify the relaxation dipersion
models
Project: relax
Submitted by: None
Submitted on: Tue 03 Jun 2014 12:25:50 PM UTC
Category: GUI
Specific analysis
Follow-up Comment #2, bug #22131 (project relax):
relax 3.2.1
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2014 the relax development team
This is free
URL:
http://gna.org/bugs/?22257
Summary: Slowness/Hanging while editing free format file
settings
Project: relax
Submitted by: None
Submitted on: Tue 01 Jul 2014 09:18:18 PM UTC
Category: GUI
Specific analysis category:
URL:
http://gna.org/bugs/?22730
Summary: Relax stop and quit at polate step
Project: relax
Submitted by: None
Submitted on: mar 30 set 2014 09:00:24 UTC
Category: None
Specific analysis category: Model-free analysis
Follow-up Comment #2, bug #22730 (project relax):
Thanks for your quick and promtp reply,
Here are the answers to your questions:
1) No, they did not stop at the same point, Xubuntu stopped at the point of
'Obate' 5 rounds.
2) Couldn't find log file. See 3).
3) Done for both Xubuntu and
Follow-up Comment #5, bug #22730 (project relax):
No no, it is running now as I started a new session. I just wanted to show you
the first messages, where you can see that some of the spins were deselected
'because of the absense of relaxation mechanisms' (written in red as
RelaxWarnings). My
Follow-up Comment #6, bug #22730 (project relax):
Hi Edward,
I am back with some results from the calculations I began two weeks ago. Just
to remind, I am running the Model-free analysis on the 73 AA protein domain at
three magnetic fields. Relax is running using 7 slaves. However, the
Follow-up Comment #8, bug #22730 (project relax):
The compressed bz2 log file is too big currently (around 3 Mb)so I took the
first part that would be compressed to around 1 Mb. I just decompressed the
bz2 file, cut the first part to zip within 1Mb.
Olena
(file #22627)
Follow-up Comment #10, bug #22730 (project relax):
Thanks! I will upgrade the Relax version. Perhaps, it will solve the entire
problem.
Answering your questions, I use local harddisk. I ran Relax through a GUI
interface. I start with typing (in the defined directory):
mpirun -np 8
Follow-up Comment #12, bug #22730 (project relax):
Hi,
I have no idea why the information containing the data and its specification
is missing. I follow the protocol loading the DC files (after I load the H and
N spins from the pdb file), specifying all the parameters (temperature control
etc.).
Follow-up Comment #15, bug #22730 (project relax):
I attached the file you requiested (file_listing).
(file #22643)
___
Additional Item Attachment:
File name: file_listing Size:7 KB
Follow-up Comment #22, bug #22730 (project relax):
Dear Edward,
I have been running the analysis of the entire protein this time for more than
two weeks from now. And we had a power blackout. How can I restart my
calculatioins? What is the right command?
Olena
Follow-up Comment #23, bug #22730 (project relax):
Thanks!
I have started the program once again.
I wonder, does Relax have a sample data of the known (short) protein to use as
an example. So that it is possible to load and run these data within a short
time and later analyse the results, just
URL:
http://gna.org/support/?3219
Summary: Help for inputting CPMG dispersion data from heigh
list
Project: relax
Submitted by: None
Submitted on: Tue 10 Mar 2015 02:30:42 AM UTC
Category: None
Priority: 5
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