[Chimera-users] Double chain IDs

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 8 09:13:51 PDT 2019

Dear Albert,
There is an open ticket for ChimeraX (but not Chimera, as far as I know) to handle 2-character chain IDs, i.e. it is still on the “to do” list.  Most development efforts these days are on ChimeraX, and it is faster on large systems than Chimera anyway.  If you may be interested in using ChimeraX, you can check progress of the ticket here:

It’s slightly tricky to implement because the “extra” column is used for special residue names by some software, so there need to be some rules to distinguish between that possibility and when the column is used for the 2-character chain IDs.

Both Chimera and ChimeraX have an option to write PDB using “h36” numbering that incorporates alphabetical characters for atom/res, but without touching the chain IDs:

ChimeraX can also write mmCIF, with some limitations:

I am not sure what’s going on with your ATOM change to HETAM… it must be that Chimera “thinks” those are HET residues, but we may need an example to understand the details.  I hope this clarifies the situation,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 8, 2019, at 2:08 AM, Albert WEIXLBAUMER <weixlbau at igbmc.fr> wrote:
> Dear Chimera developers,
> My apologies if this question has been asked before but I was not able to find an answer so far.
> I am dealing with PDB files that contain too many individual chains and as such need two-character chain IDs. Ideally I do not want to split the PDB-files (to be able and work with single-character chain IDs). In addition, the PDB-file also contains more than 100,000 atoms and thus uses alphanumeric atom numbers.
> It seems Chimera is not aware of the two-character chain IDs because selecting a certain chain in the GUI shows only single character chain IDs and it leads to the selection of the two distinct chains (e.g. chain AA and chain BA are both treated as chain A). Is there a workaround?
> I’ve also noticed that saving such a PDB-file in Chimera changes all ATOM records to HETATM - I don’t know if this is related to the double-character chain IDs or alphanumeric atom numbers but this causes problems downstream because it’s very difficult to change this back to ATOM records without also affecting true HETATM entries.
> Thank you for your help!
> Best regards,
> Albert

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