[Chimera-users] Chimera user advice

Wil Ratzan wilratzan at gmail.com
Thu Feb 15 23:02:49 PST 2018

Elaine and Aldo,

Your advice was spot-on and I was able to quickly map conserved residues
onto our protein's crystal structure by saving an alignment that I made as
an .aln file and then opening it concurrently with the crystal structure
.pdb file in Chimera.

Thanks for providing such great software and support!


On Mon, Feb 12, 2018 at 11:01 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
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