[Chimera-users] Unstructured residues disappear from sequence after save and reopen

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 23 08:46:40 PDT 2020

Hi Rob,
If you open 6vxx as PDB format (not mmCIF) and then save PDB, it will preserve the SEQRES information including the residues without coordinates.

It is a bug that opening from mmCIF and then saving a session or PDB does not save this information, but most effort is now on ChimeraX.  In ChimeraX, saving a session after opening a structure from mmCIF saves the sequence info, but saving a PDB file does not, so I will open a ChimeraX bug ticket for that.

Sorry for the inconvenience,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 23, 2020, at 7:02 AM, Rob Blakemore <robert.blakemore at tufts.edu> wrote:
> Hi,
> I'm encountering a problem wherein unstructured residues are present in the sequence the first time I fetch it from PDB, but are omitted after I save the file locally and reopen it. Has anyone else encountered this and would you happen to know a workaround?
> Details
> I'm running Chimera 1.14 (build 42094)  on MacOS Mojave V10.14.6
> I'm using 6VXX as the PDB file.
> When I fetch a structure by ID: (PDB mmCIF) and open a sequence (Tools --> Sequence --> Sequence), it shows me a complete sequence containing both residues present in the structure, as well as unresolved/unstructured residues. The unresolved residues are outlined by a red border.
> However, if I save this session to a file or save the structure to PDB and then reopen it; if I then open the sequence, it only shows me the sequence of residues present in the structure, and omits all of the unresolved / unstructured residues. (All the red outlined residues are now gone)
> Is there any way to preserve the unstructured residues when saving these files? 
> Thank you,
> Rob Blakemore
> robert.blakemore at tufts.edu
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