Hi Edward, With revision 14802 the script seems to work, provided the "spin_num_col=4" is removed from "sequence.read" and "relax_data.read".
Thank you, Vitaly On Wed, Oct 5, 2011 at 11:18, Edward d'Auvergne <[email protected]> wrote: > 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
