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/relax-commits@xxxxxxx/msg06219.html).
Also, if possible, could you append "OT" atom name (XPLOR format) to
the oxygen list?
Thank you,
Vitaly
Problem with "CH2" atom