[Chimera-users] two-letter ID of polypeptide

[Eric Pettersen]

Our plan is that after reading all ATOM/HETATM records, check to see if interpreting column 21 as part of the chain ID produces consistent chain IDs within each TER-card-delimited section.  If it does, then treat that column as part of the chain ID.  Otherwise, treat it as part of the residue name.  We will implement that in both Chimera and ChimeraX (since the PDB-reading code for both is very similar), but it may be some time before we get to it.  I will open a feature-request ticket for this in our bug-tracking database and include you in the recipient list, so you will be notified when it gets implemented.

—Eric

> On Apr 17, 2019, at 1:27 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> We are discussing possible options internally, but FYI Amber and Amber-compatible programs frequently make use of 4-character residue names for terminal amino acids (e.g. NALA, CALA).
> 
> —Eric
> 
>> On Apr 17, 2019, at 1:01 AM, Pu Qian <p.qian at sheffield.ac.uk> wrote:
>> 
>> 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
>> 
>>        Eric Pettersen
>>        UCSF Computer Graphics Lab
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