[Chimera-users] Chimera renumbering residues in mol2 file

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 21 08:53:19 PDT 2020

I changed the "Subject" line to something useful.

Chimera does not automatically renumber the protein residue sequence.

I tried opening 5trf directly from the PDB and the chains start numbering at 10, for example chain A shown with commands:

open 5trf
~ribb ~:.a
rl :1-20

I agree that using "File... Save Mol2" renumbers the residues in the Mol2 file.  

However, if you use "File... Save PDB" it does not renumber, so unless you have some other reason for using Mol2, save as PDB instead.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 21, 2020, at 12:23 AM, Samiha I Amer <lanre.durojaye at yahoo.com> wrote:
> Hello
> Please how do I prevent chimera from renumbering my protein residue sequence in cases where I am working with a pdb structure that does not cover all the residues?
> For example, the attached pdb protein file (5trf.pdb) was downloaded from the pdb database with the first 9 residues missing. The first residue in the pdb structure is the 10th residue and this was numbered accordingly but whenever I upload such structures on Chimera, the numbering of the residues tend to scatter because chimera automatically numbers the first residue in the structure as 1, just as it appeared in the attached mol2 file.
> Please how do I avoid/correct such
> Thank you.
> <5trf.pdb><5TRF.mol2>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200821/51d62ee5/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 5trfa.png
Type: image/png
Size: 53443 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200821/51d62ee5/attachment-0001.png>

More information about the Chimera-users mailing list