URL:
<http://gna.org/bugs/?11378>
Summary: relax_data.back_calc raises errors
Project: relax
Submitted by: rydog
Submitted on: Wednesday 03/26/2008 at 17:44
Category: None
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: 1.2.12
Operating System: GNU/Linux
_______________________________________________________
Details:
The session is replicated below; the two attachments have the script and two
small PDB that demonstrate the problem and perturb it.
So if "bugdemo2.pdb" is used, that's the original problem I noticed, which
raises the error:
"RelaxError: The unit XH bond vectors for the run 'dummyMF' have not been
calculated."
If "bugdemo3.pdb" is used instead (that PDB lacks the first residue which is
a protonated aminoterminus) the error message changes to:
"RelaxError: The type of nucleus has not yet been set."
Here's the session (with bugdemo2.pdb):
relax bug1.rlx
ImportError: relaxation curve fitting is unavailible, try compiling the C
modules.
?1034h
relax 1.2.12
Protein dynamics by NMR relaxation data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
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'. Assistance
in using this program
can be accessed by typing 'help'.
script = 'bug1.rlx'
----------------------------------------------------------------------------------------------------
#trying to use relax to calculate expected relaxation values given a pdb and
its diffusion tensor
run.create('dummyMF','mf') #dummy model free run
pdb(run='dummyMF',file='bugdemo2.pdb',dir='~/work/RELAX/',proton='HN')
model_free.create_model(run='dummyMF',model='m1',params=['S2'],equation='mf_orig')
diffusion_tensor.init(run='dummyMF',params=(2.405e06,2.463e06,7.986e06,80,80,60),param_types=2,fixed=1)
relax_data.back_calc(run='dummyMF',ri_label='R2',frq_label='800',frq=800.)
----------------------------------------------------------------------------------------------------
relax> run.create(run='dummyMF', run_type='mf')
relax> pdb(run='dummyMF', file='bugdemo2.pdb', dir='~/work/RELAX/',
model=None, heteronuc='N', proton='HN', load_seq=1)
Loading all structures from the PDB file.
Structure('/home/rydog/work/RELAX//bugdemo2.pdb'):
Peptide chain of length 3
Loading the sequence from the PDB file.
Calculating unit XH vectors.
Structure 1
RelaxWarning: The atom HN could not be found for residue 1
Calculating the unit XH vectors from the structure.
relax> model_free.create_model(run='dummyMF', model='m1', equation='mf_orig',
params=['S2'], res_num=None)
relax> diffusion_tensor.init(run='dummyMF', params=(2405000.0, 2463000.0,
7986000.0, 80, 80, 60), time_scale=1.0, d_scale=1.0, angle_units='deg',
param_types=2, spheroid_type=None, fixed=1)
relax> relax_data.back_calc(run='dummyMF', ri_label='R2', frq_label='800',
frq=800.0)
RelaxError: The unit XH bond vectors for the run 'dummyMF' have not been
calculated.
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Wednesday 03/26/2008 at 17:44 Name: bug1.rlx Size: 489B By: rydog
<http://gna.org/bugs/download.php?file_id=4047>
-------------------------------------------------------
Date: Wednesday 03/26/2008 at 17:44 Name: bugdemo3.pdb Size: 2kB By:
rydog
<http://gna.org/bugs/download.php?file_id=4048>
-------------------------------------------------------
Date: Wednesday 03/26/2008 at 17:44 Name: bugdemo2.pdb Size: 3kB By:
rydog
<http://gna.org/bugs/download.php?file_id=4049>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?11378>
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