[Chimera-users] Chimera user advice

[Wil Ratzan]

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!

-Wil

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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