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
