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

[Rob Blakemore]

Thank you so much for the answer. This does indeed solve my problem.

All the best,
Rob

On Mon, Mar 23, 2020 at 11:47 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> -----
> 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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