[Chimera-users] two-letter ID of polypeptide

[Pu Qian]

Hi Eric,

It sounds good. It will definitely be helpful for all chimera users who is
dealing with very big complexes.

Best regards

Pu Qian

On Mon, 22 Apr 2019 at 23:02, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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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