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
