[chimerax-users] Color protein by residue

[Tom Skillman]

Hi Elaine,



I guess I was asking both questions: 1) Is it possible to color a PDB protein by residue, i.e. each of the 23 residues as a different, but consistent, color across the whole protein, and 2) Do you support any of the standard color schemes like this one that I've used in the past –



[cid:image002.jpg at 01D31FF0.B3613260]



I'm more interested in the first issues - can I color ByResidue (with any color scheme)?   ☺



Thanks for your assistance.



Best,

Tom



Thomas Skillman

Director Research Technology

Benaroya Research Institute for Autoimmune Disease

Seattle, WA



PS – If you are interested, I created an VR based immersive space for collaborating on PDB models. It adds another dimension to looking at and discussing protein structure.  Let me know if you’re interested and we can set up a time to give you a demo.









-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Sent: Monday, August 28, 2017 9:59 AM
To: Tom Skillman <TSkillman at benaroyaresearch.org>
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] Color protein by residue



Hi Tom,

I don’t know what you mean by standard colors.  There is “color byelement” for using element color-coding of atoms, “color byhet” for leaving carbons unchanged and element color-coding the other atoms.  The element colors are shown here:

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#element>



There is no set of standard colors indicating the amino acid types, if that’s what you meant, at least not in ChimeraX.  That may be the reason you couldn’t figure it out.  :-)



I hope this clarifies,

Elaine

----------

Elaine C. Meng, Ph.D.

UCSF Chimera(X) team

Department of Pharmaceutical Chemistry

University of California, San Francisco





> On Aug 27, 2017, at 8:30 PM, Tom Skillman <TSkillman at benaroyaresearch.org<mailto:TSkillman at benaroyaresearch.org>> wrote:

>

> I can’t figure out the command for coloring the proteins of a protein with standard colors.. Can you help?  Thx.



________________________________
--CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20170828/103e548d/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.jpg
Type: image/jpeg
Size: 74200 bytes
Desc: image002.jpg
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20170828/103e548d/attachment.jpg>