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

Greg Couch gregc at cgl.ucsf.edu
Fri Jan 18 08:44:22 PST 2019

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, 

What program is doing the PDB to mmCIF conversion?



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/
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