[Chimera-users] icosahedral reconstruction volume color

[Reginald McNulty]

Hi Elaine,

I'm wondering if I can color just the five-fold vertices of my icosahedral surface red, without coloring the entire surface red.

Reggie
______________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, September 20, 2012 9:22 AM
To: Reginald McNulty
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] icosahedral reconstruction volume color

Dear Reggie,
I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me.

You can open and display the vol file in Chimera, assuming it is the SPIDER format:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>

You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor".
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>

These support coloring by
(a) map value or gradient norm
(b) distance from a point, axis or plane

radial coloring = coloring by distance from a point, where the point is the center of symmetry

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

On Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote:

> Dear Users,
> I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry?
> Kind regards,
> Reggie