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

Carmen San Martin carmen at cnb.csic.es
Fri Jan 18 04:06:22 PST 2019

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.

  Carmen San Martín, Ph. D.
  Centro Nacional de Biotecnología (CNB-CSIC)
  Darwin, 3
  28049-Madrid (SPAIN)
  Email:  carmen at cnb.csic.es
  Phone:  34-91-5855450
  Fax:     34-91-5854506 <http://www.cnb.csic.es/>
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