[Chimera-users] two-letter ID of polypeptide

Pu Qian p.qian at sheffield.ac.uk
Wed Apr 17 01:01:01 PDT 2019

Hi Eric Pettersen,

Thanks for your emails.
 I understand that current version of chimera still only use one letter ID,
and column 21 is for 4-letter residues. The problem is: in current version
of COOT, user can assign two-letter to a polypeptide, and the column 21 is
used for it. When pdf file was output from COOT, than chimera can not use
the pdb file as we expected. It could be better to use column 21 for
two-letter ID. After all, very few people will use 4-letter residues. In
this way,  chimera still can be used for visualisation of the COOT
two-letter ID pdb file, which can be convert to mmCIF format. Before
conversion, we need to view it making sure there are no problems.
Otherwise, it is not convince for uses who are working on bigger complex
that has more than 62 polypeptides.

Best regards

Dr. Pu Qian

To elaborate a little on this, column 21 in an ATOM record is unassigned
and Chimera conscripts that column to allow for 4-character residue names
rather then 2-character chain IDs (the former were more far common a
million years ago when Chimera was originally designed).  So knowing that
that column is part of the residue name may help you work around some
things.  For instance PDB residue name LIG in chain AB will be treated by
Chimera as residue name LIGA in chain B (so, an atom spec of :LIGA.B rather
than :LIG.AB).


        Eric Pettersen
        UCSF Computer Graphics Lab
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