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

[Carmen San Martin]

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
  Phone:  34-91-5855450
  Fax:     34-91-5854506 <http://www.cnb.csic.es/>
  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> 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
>   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
> 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/20190121/9395f0a1/attachment.html>