[Chimera-users] how to get chimera to use the auth_seq_id in .cif format files

[Greg Couch]

Sorry, I don't use biopython.  You should submit a bug with biopython, 
or better yet, fix it, and submit a patch :-). The entity_poly_seq mmCIF 
table is roughly equivalent to the PDB SEQRES records.

Also, why use mmCIF?  If biopython's PDB writer is better, then use it.  
Chimera's PDB reader is much faster than its mmCIF reader.  ChimeraX's 
mmCIF reader is faster than its PDB reader (at least it was, haven't 
measured recently).  If you need to convert a PDB file to an mmCIF file, 
try using ChimeraX, http://www.rbvi.ucsf.edu/chimerax/. And if you find 
a mmCIF bug in ChimeraX, submit a bug report and we'll fix it.

     HTH,

     Greg

On 1/21/2019 2:49 AM, Carmen San Martin wrote:
> Hi Greg,
>
> you are correct, we do not have entity_poly_seq. We are using 
> biopython for the conversion, but we have not been able to figure out 
> how to create that particular table. Any hints will be welcome!
>
> Best,
> -------------------------------------------------------------
>   Carmen San Martín, Ph. D.
>   Centro Nacional de Biotecnología (CNB-CSIC)
>   Darwin, 3
>   28049-Madrid (SPAIN)
>   Email: carmen at cnb.csic.es <mailto:carmen at cnb.csic.es>
>   Phone:  34-91-5855450
>   Fax:     34-91-5854506
> http://tinyurl.com/carmensanmartinlab
> https://sites.google.com/site/adenonet/
> ------------------------------------------------------------
>
>
> On Fri, Jan 18, 2019 at 5:44 PM Greg Couch <gregc at cgl.ucsf.edu 
> <mailto:gregc at cgl.ucsf.edu>> wrote:
>
>     The PDB file is being incorrectly converted to a mmCIF file. 
>     Without seeing the two files, I can not say for sure, but it is
>     mostly like that the entity_poly_seq table is missing or
>     incomplete.  Chimera uses the auth_seq_id to identify the
>     residues, but uses label_seq_id to connect the residues.  So if
>     the sequence for the gap residues is missing, and the
>     label_seq_id's are consecutive, then the residues are adjacent,
>     i.e, connected.
>
>     What program is doing the PDB to mmCIF conversion?
>
>         HTH,
>
>         Greg
>
>     On 1/18/2019 4:06 AM, Carmen San Martin wrote:
>>     Hi all,
>>     I am using chimera to display a structure with a 10-residue gap.
>>     When I use a pdb format file, the gap appears as a dashed line
>>     and everything is fine. However, when I convert the coordinate
>>     file to cif format, chimera draws a very long bond across the
>>     gap. Further, the residue numbering seems to have changed, so
>>     that now instead of skipping the 10 figures in the gap, the
>>     residues at both sides are consecutively numbered, and therefore
>>     the numbering in the rest of the protein is wrong. I understand
>>     this happens because chimera is using the cif column
>>     "label_seq_id" instead of "auth_seq_id" to identify the residue
>>     number. Is there a way to make chimera use the auth_seq_id column
>>     instead?
>>
>>     Sorry if this has already been answered, I googled it and saw
>>     similar questions but not the actual answer to this one.
>>
>>     Best,
>>     -------------------------------------------------------------
>>       Carmen San Martín, Ph. D.
>>       Centro Nacional de Biotecnología (CNB-CSIC)
>>       Darwin, 3
>>       28049-Madrid (SPAIN)
>>       Email: carmen at cnb.csic.es <mailto:carmen at cnb.csic.es>
>>       Phone:  34-91-5855450
>>       Fax:     34-91-5854506
>>     http://tinyurl.com/carmensanmartinlab
>>     https://sites.google.com/site/adenonet/
>>     ------------------------------------------------------------
>>
>>     _______________________________________________
>>     Chimera-users mailing list:Chimera-users at cgl.ucsf.edu  <mailto:Chimera-users at cgl.ucsf.edu>
>>     Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190121/177fe404/attachment.html>