Hi Greg,

Thanks a lot for the clarification. I can only say from experience that ChimeraX mmCIFs throw an error upon upload due to the lack of entity_poly.pdbx_strand_id. If I copy it from a previous PDB generated file into the header using a text editor, the upload works fine.
Regarding the sheets, the lack of sheets does not generate an upload error for the PDB.
I tried the computeSheets true option through the GUI and it never worked – I just found a bug that when you click the”Computed sheets” check box in the save dialog, ChimeraX passes the wrong command:

save "Models/For_Deposition/test.cif" models #2 fixedWidth false computeSheets true

Expected a keyword

If I manually edit it to “computedSheet”  then the saving works.

Thanks and best wishes,

Matthias

From: Greg Couch <gregc@cgl.ucsf.edu>
Date: Thursday, July 11, 2024 at 22:55
To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>, ChimeraX-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] ChimeraX generated mmCIF files not suitable for PDB deposition

The PDB's documentation for entity_poly.pdbx_strand_id says it is not required -- https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_entity_poly.pdbx_strand_id.html.   And the documentation is says it is: "The PDB strand/chain id(s) corresponding to this polymer entity."  That seems poorly defined.   I'll ask the PDB for clarification.  I am surprised that the PDB is requiring entity_poly,pdbx_strand_id, since it should be computable from the rest of the file.  And if they computed it, there would be no ambiguities.

But even if that is fixed, I suspect that the PDB will still have issues with the fact that ChimeraX outputs all sheet ids as unknown.  And that is because ChimeraX currently does not keep track of the sheets, only the strands.  To get unique sheet ids, give the "computsedSheets true" option -- "save foobar.cif computedSheets true".  Then the mmCIF writer will run the DSSP computation and use that to generate the sheet/strand information.  But that overrides any choices that were in the input file.

    HTH,

    Greg

On 7/11/24 12:52, Vorländer,Matthias Kopano via ChimeraX-users wrote:

Dear ChimeraX team,

Structure files in .cif format that are generated by ChimeraX are unfortunately not suitable for deposition to the PDB. This is due to lack of the column _entity_poly.pdbx_strand_id in the header. The column is usually found in the header in this table and contains the chain Identifier (i.e ‘A’ for chain A):

loop_

_entity_poly.entity_id

_entity_poly.nstd_monomer

_entity_poly.type

_entity_poly.pdbx_seq_one_letter_code_can

Since ChimeraX does an excellent at converting PDBs to mCIFs otherwise, would it be possible to have ChimeraX include this column in the header of mmCIF files?  This would greatly help to facilitate the tiresome process of depositing models to the PDB.

Many thanks in advance,

Best,

Matthias