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@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@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@tufts.edu

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Marta, Rob, The underlying problem is that both Chimera and ChimeraX’s PDB code “preserves” sequence information simply by saving any SEQRES records that were present in the original input. mmCIF files do not have SEQRES records and therefore no such records make it into a PDB file saved from an mmCIF structure. Neither program looks at the structure per se to generate the SEQRES records. So what needs to happen is that instead of simply passing through pre-existing SEQRES records, the programs need to look at the structures being saved and construct corresponding SEQRES records. We have a ticket open for this in ChimeraX, and we will fix it. It might also be done in Chimera, but it’s less likely (depends on the difficulty). --Eric Eric Pettersen UCSF Computer Graphics Lab

On Mar 23, 2020, at 10:20 AM, Marta Perez Illana <marta.perez@cnb.csic.es> wrote:

Hi Rob

I was having exactly the same situation as you mention... Same here if I save those mmCIFs in regular chimera as PDBs, unstructured sequence is somehow lost.

The only think I could do was use chimerax, where the unstrucutred sequence is kept after saving it as a mmCIF format.

and then I open it and the whole sequence is kept. If I play around with the mmCIF in chimerax everything is fine and kept and can use it normally. But If I would open it in traditional chimera, unstructured sequence would be kept, but again, when saving it, the unstructured sequence is lost.... But this is NOT when saved in PDB format. Like if you would save in PDB format in chimerax no unstructured sequence is neither kept, as in traditional chimera...

I think ( and this is just a practical opinion, since I lack the theory underneath) that this has something to do with the new mmCIF files format. At least everything that I usually fetch nowadays are mmCIF already (even if in the past they were initially PDBs in the data base).

If there is an alternative way I would also be more than interested :)

Regards

Marta

On 23.03.20 15:02, Rob Blakemore 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@tufts.edu <mailto:robert.blakemore@tufts.edu>

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

-- Marta Pérez Illana, Ph. D. student Dept. of Macromolecular Structures Lab 15 Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: marta.perez@cnb.csic.es <mailto:marta.perez@cnb.csic.es> Phone: (0034) 91 585 4508 http://wwwuser.cnb.csic.es/~sanmartinlab <http://wwwuser.cnb.csic.es/~sanmartinlab>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users