[Chimera-users] Chimera user advice

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 12 10:01:38 PST 2018


Hello Wil,
If you just mean that you don’t know how to specify or select individual residues, there are many ways…. some are outlined in this recent post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-February/014344.html>

Command “color red :258.A” would color residue 258 in chain A red, for example.

Also, if you are showing the sequence, another way to select a specific residue is by using the mouse to drag a box around it in the sequence.

If you have a sequence alignment already, it is easy to show the conservation from that alignment on the structure.  This tutorial is all about mapping sequence conservation:
<https://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>

If you never showed sequence alignments in Chimera before, this tutorial helps get you started, and it also has a color-by-conservation example at the end:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>

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

> On Feb 12, 2018, at 3:38 AM, Wil Ratzan <wilratzan at gmail.com> wrote:
> 
> Hello,
> I truly appreciate the development and distribution of software such as Chimera to the scientific community, but alas I am not 'computer-savvy.'
> 
> I would like to map highly conserved residues of a protein onto its crystal structure (PDB 3V0I). I can view the PDB file of the crystal structure using Chimera, but I am having a hard time figuring out how to highlight residues. Could you please give me some advice about how to identify and mark particular residues using this file?
> 
> I apologize if this request seems trivial, and I appreciate any advice.
> Thanks,
> -Wil Ratzan




More information about the Chimera-users mailing list