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> _______________________________________________ Message sent via/by Gna! http://gna.org/