Sarma,
I am trying to create a surface representation of a protein with
mutations that abolish activity in one color (say yellow) and the ones
that don't change activity in another (say green). The rest of the
residues colored gray.
I can change the color of the surface to gray or a rainbow gradient
using the options but can't find a way to specify the residues that
need to be colored differently in a surface representation.
One easy way to go about coloring residues differently based on some
property like a residue number is to create atom selections for the
various sets of residues in which you're interested and then color those
selections using the PyMOL menu commands... Look in the "Command Syntax
and Atom Selections" section of the PyMOL User's Manual
(http://pymol.sourceforge.net/newman/user/toc.html) in order to learn
about atom selections. You can enter a command like "select mymuts, all
and resi 23,32,45" to create a selection consisting of all atoms in
residues 23, 32, and 45, and then something like "color green, mymuts"
to color these residues green. So something like this might be what you
want:
select mymut, (resi 23,32,45)
select mywt, (resi 1,2,3,4,5)
color grey, all
color yellow, mymut
color green, mywt
If you don't foresee needing the atom selections for anything else, you
could just combine the atom selection with the color command ("color
yellow, (resi 23,32,45)"), but it's most often useful to create an
independent atom selection.
If you want to color even more precisely by a parameter such as the
strength of the mutant's inactivity -- so multiple values instead of
just 0/1 -- then you could try looking at the Sequence Conservation
example on my PyMOL page (this is documented at
http://mccammon.ucsd.edu/~cmura/PyMOL for now; I'll eventually migrate
this stuff into PyMolWiki and post updates of new stuff at
http://www.pymolwiki.org/index.php/Cmura).
Good luck,
Cameron
=== pymol-users-requ...@lists.sourceforge.net wrote (on 04/03/2005 08:19
PM): ===
Today's Topics:
1. surface representation showing mutations (Ganapathy Sarma)
Subject:
[PyMOL] surface representation showing mutations
From:
Ganapathy Sarma <gnsa...@gmail.com>
Date:
Sun, 03 Apr 2005 18:13:49 -0700
To:
pymol-users@lists.sourceforge.net
Hello PYMOLers,
I am a very new entry to the world of Pymol after seeing the program
in action at a recent conference.
I am trying to create a surface representation of a protein with
mutations that abolish activity in one color (say yellow) and the ones
that don't change activity in another (say green). The rest of the
residues colored gray.
I can change the color of the surface to gray or a rainbow gradient
using the options but can't find a way to specify the residues that
need to be colored differently in a surface representation.
Any help is appreciated.
Thanks,
Sarma
