Hi, I have just looked at the code, and the recent change I made with the spin_id was incorrect. It should now be fixed by r14792. I'll have a look at the bug report and try to reproduce the bug now.
Cheers, Edward On 5 October 2011 18:07, V.V. <[email protected]> wrote: > Hi Edward, > > Thank you for your comments. The "relax_data.read" actually included > reading the data and errors (so much for copy-pasting). I have updated > the relax version to rev. 14791 and the error message now is > "UnboundLocalError: local variable 'spin_id' referenced before > assignment". > I have submitted a bug report with an example attached (#18790). > > Vitaly > > On Wed, Oct 5, 2011 at 04:03, Edward d'Auvergne <[email protected]> wrote: >> Hi Vitaly, >> >> The problem here is not to do with the spin numbering. That is not >> needed. I've now updated relax to print out the full spin ID string >> instead of just the spin number and name. I've also modified the >> error messages to be more informative. Could you update your >> repository copy of relax and send the new error messages? Thanks. >> One problem I see, though this may not be the cause of the error, is >> in the reading of the relaxation data. The script line: >> >> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.484*1e6, >> file='data.r1.600', mol_name_col=1, res_num_col=2, res_name_col=3, >> spin_name_col=5) >> >> should probably be: >> >> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.484*1e6, >> file='data.r1.600', mol_name_col=1, res_num_col=2, res_name_col=3, >> spin_name_col=5, data_col=6, error_col=7) >> >> Specifying the data and error columns is very important. Though >> according to the code, if the data and error were not read in, then >> the checks resulting in the RelaxError should not occur. The problem >> with the spin numbers is that the numbers in 'data.r1.600' do not >> match the numbers in the first column of the PDB file. For proteins, >> it is safe to not specify the spin number as all atoms of the residue >> should have a different name. For small organic molecules, RNA, DNA, >> sugars, etc, this is not the case. Anyway, the spin numbers in the >> structural file and data files must match if they are used at all. >> >> If you could, submitting a bug report would be appreciated >> (https://gna.org/bugs/?func=additem&group=relax). This helps other >> relax users if they encounter the same issue. If you could attach a >> minimal script with a minimal data set (relaxation data for one or two >> residues, randomised if you prefer), then I'll be able to quickly >> reproduce the bug and normally fix it within 5 minutes. I would then >> also be able to add the script and data to the relax test suite to >> make sure that the bug never returns. >> >> Cheers, >> >> Edward >> >> >> >> >> On 5 October 2011 01:48, V.V. <[email protected]> wrote: >>> Hello, >>> >>> It looks like Relax scripts changed a bit since the last time I used >>> it. I am trying to setup the initial test calculation with >>> "single_model.py", and running into problems with spins initialization >>> (revision 14778). >>> >>> Sample input files: >>> ===== >>> #mol_name res_num res_name spin_num spin_name data error >>> ave 1 Met 1 N None None >>> ave 2 Glu 2 N 1.8903 0.06062 >>> ... >>> ===== >>> >>> Script extract is below: >>> ===== >>> name = 'tm1' >>> pipe.create(name, 'mf') >>> >>> sequence.read('data.r1.600', mol_name_col=1, res_num_col=2, >>> res_name_col=3, spin_name_col=5) >>> structure.read_pdb('ave.pdb', read_mol=1, set_mol_name='ave', >>> parser='internal') >>> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.484*1e6, >>> file='data.r1.600', mol_name_col=1, res_num_col=2, res_name_col=3, >>> spin_name_col=5) >>> >>> #More data sets are loaded and other parameters initialized >>> Grid_search(inc=11) >>> ===== >>> >>> This returns an error: >>> "RelaxError: Negative error for spin 'None N', minimization not possible" >>> >>> Is this because the "spin_number" has not been initialized during the >>> "sequence.read" and "relax_data.read"? If I try to use >>> "spin_num_col=4" in "sequence.read", then "structure.read" returns an >>> error: "RelaxWarning: Cannot find the atom in the structure (atom ID >>> ':2@2&@N')" >>> >>> Please let me know if you need more details. >>> >>> Thank you, >>> Vitaly >>> >>> _______________________________________________ >>> 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 > _______________________________________________ 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
