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
