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