Hi, The addition of spin_id='@N' should not be necessary if the sequence data you have loaded using this script has the atom/spin name set to 'N'. If not, I have modified the full_analysis.py script in the repository 1.3 line to name your spins in that way. The problem is that the spins are unnamed so they cannot be matched to anything in the PDB file. Hence the NH bond vectors are not extracted for any spins. Then when it comes to optimisation, all the spins without bond vector information are deselected. But as this is all spins, then there are essentially no model-free models to optimise and there is only the diffusion tensor. But this is fixed by the fix() function, the one you can't fix and can't be fixed. So as the only parameters remaining are those of the diffusion tensor, and these are fixed, relax cannot do anything. There should be warning messages describing this problem much further up in the script. I would guess thought that they have been suppressed by your addition in point one, as there are no spins with a spin id of '@N' and hence no NH bond vectors will be loaded.
Regards, Edward On Tue, Feb 10, 2009 at 5:00 PM, Pierre-Yves Savard <[email protected]> wrote: > Hi, > > I am starting a new relax analysis with the full_analysis.py script, > together with relax 1.3 revision 8769. I performed the first step, > 'local_tm', with success. > > However, for what concerns diffusion models 'sphere', 'prolate', 'oblate > and 'ellipsoid', I encountered the following errors: > > 1. I had to add: "spin_id='@N'" in the function structure.vector() > in order to read the pdb and extract vectors properly: > > > # Load the PDB file and calculate the unit vectors parallel to > the XH bond. > if not local_tm and PDB_FILE: > structure.read_pdb(PDB_FILE) > structure.vectors(attached='H', spin_id='@N') > > ... > > # Load the PDB file and calculate the unit vectors parallel to > the XH bond. > if PDB_FILE: > structure.read_pdb(PDB_FILE) > structure.vectors(attached='H', spin_id='@N') > > > 2. Then, I encountered the following error message (using the debug > option -d) when trying to optimise models 'prolate', 'oblate' and > 'ellipsoid': > > Traceback (most recent call last): > File "full_analysis_prolate.py", line 640, in <module> > Main(self.relax) > File "full_analysis_prolate.py", line 267, in __init__ > self.multi_model() > File "full_analysis_prolate.py", line 631, in multi_model > grid_search(inc=GRID_INC) > File "/usr/local/packages/relax-1.3/prompt/minimisation.py", line 156, > in grid_search > minimise.grid_search(lower=lower, upper=upper, inc=inc, > constraints=constraints, verbosity=verbosity) > File "/usr/local/packages/relax-1.3/generic_fns/minimise.py", line > 185, in grid_search > grid_search(lower=lower, upper=upper, inc=inc, > constraints=constraints, verbosity=verbosity) > File > "/usr/local/packages/relax-1.3/specific_fns/model_free/mf_minimise.py", > line 479, in grid_search > self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, > constraints=constraints, verbosity=verbosity, sim_index=sim_index) > File > "/usr/local/packages/relax-1.3/specific_fns/model_free/mf_minimise.py", > line 788, in minimise > model_type = self.determine_model_type() > File "/usr/local/packages/relax-1.3/specific_fns/model_free/main.py", > line 1026, in determine_model_type > raise RelaxError, "All parameters are fixed." > RelaxError: RelaxError: All parameters are fixed. > > > There seems to be a problem with the fix() function, although I was not > able to fix (!) it... > > Thank you very much for your help, > > > Pierre-Yves > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > [email protected] > > 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 > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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
