Thank you, Edward. If I come across more unusual atom names, I will let you know. :-)
Vitaly On Tue, Jan 11, 2011 at 03:03, Edward d'Auvergne <[email protected]> wrote: > Ok, this should now be fixed. If you have any other atom names that > could be included, that would be quite useful. If you like and have > the time, maybe you could even make the changes yourself on an SVN > copy of relax and send the patch file ($ svn diff > patch) to be > applied to the 1.3 main line. > > Cheers, > > Edward > > > On 19 December 2010 05:20, V.V. <[email protected]> wrote: >> Edward, >> >> It looks like the digits are stripped from the element name in >> generic_fns/structure/internal.py, so it should be 'CH' and not 'CH2' >> in the table. Could you please update the file? >> >> Thank you, >> Vitaly >> >> >> On Fri, Dec 17, 2010 at 13:08, V.V. <[email protected]> wrote: >>> Thank you very much, Edward! >>> >>> Vitaly >>> >>> >>> On Fri, Dec 17, 2010 at 13:03, Edward d'Auvergne <[email protected]> >>> wrote: >>>> Thank you for the detailed message and creating the bug report. This >>>> is now fixed. Cheers. If you would like the changes without waiting >>>> for a new release of relax, the new code can be checked out from the >>>> repository by typing: >>>> >>>> $ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3 >>>> >>>> or if this doesn't work: >>>> >>>> $ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3 >>>> >>>> If you already have a checked out copy, try typing: >>>> >>>> $ svn up >>>> >>>> This requires installation of the subversion program >>>> (http://subversion.tigris.org/). >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> On 17 December 2010 19:52, V.V. <[email protected]> wrote: >>>>> Thank you, Edward! >>>>> I have submitted the bug report (#17343). Yes, the atom name in the >>>>> pdb file is labeled "CH2". >>>>> >>>>> Vitaly >>>>> >>>>> >>>>> >>>>> On Fri, Dec 17, 2010 at 11:38, Edward d'Auvergne <[email protected]> >>>>> wrote: >>>>>> Hi Vitaly, >>>>>> >>>>>> Thank you for identifying this problem. I just had a question, is the >>>>>> atom named 'CH2' within the PDB file? If you don't mind, would you be >>>>>> able to create a bug report for this? This would be much appreciated >>>>>> as it would help other relax users who encounter the same problem as >>>>>> you have found. This is not too important as it is a missing feature >>>>>> rather than a bug but, if you could, the bug report submission page is >>>>>> https://gna.org/bugs/?func=additem&group=relax. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> >>>>>> On 15 December 2010 02:51, V.V. <[email protected]> wrote: >>>>>>> Hello, >>>>>>> >>>>>>> I am trying to create a diffusion tensor from the results file, and I >>>>>>> am running into a following problem after >>>>>>> "structure.create_diff_tensor_pdb" is invoked: >>>>>>> >>>>>>> ================ >>>>>>> relax> structure.create_diff_tensor_pdb(scale=1.7999999999999999e-06, >>>>>>> file='tensor.pdb', dir=None, force=True) >>>>>>> Adding molecule 'diff_tensor' to model None (from the original >>>>>>> molecule number None of model None) >>>>>>> >>>>>>> Chain A >>>>>>> >>>>>>> Calculating the centre of mass. >>>>>>> RelaxWarning: Skipping the atom '#ave_mol1:2...@30' as the element name >>>>>>> does not exist in the PDB file. >>>>>>> ================ >>>>>>> >>>>>>> In the "results" file, element 30 in the atom name list is 'CH2' (Trp >>>>>>> side chain). Also if I read the structure file with >>>>>>> "structure.read_pdb", for each of the Trp residues I get: >>>>>>> >>>>>>> ================ >>>>>>> RelaxWarning: Cannot determine the element associated with atom 'CH2'. >>>>>>> ================ >>>>>>> >>>>>>> It looks like this atom was left out >>>>>>> (http://www.mail-archive.com/[email protected]/msg06219.html). >>>>>>> Also, if possible, could you append "OT" atom name (XPLOR format) to >>>>>>> the oxygen list? >>>>>>> >>>>>>> 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
