[Chimera-users] MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???

Tom Goddard goddard at cgl.ucsf.edu
Wed Aug 20 09:17:22 PDT 2008

Hi Darrell,

You need to use the multiscale coloring command "msc". Here's an example 
using Chimera commands (Favorites / Command Line):

open viperID:1p58
color blue :86.A
msc #1 :86.A 15

The first command opens a dengue virus model from the VIPERdb database. 
Then I color residue 86 of chain A blue. That just colors the atoms of 
the residue not the surface. Then the msc command colors the multiscale 
surfaces (model identifier #1 seen in Favorites / Model Panel) making 
the surface color match the blue of residue 86 within 15 Angstroms of 
that residue.

After I open the model and before coloring it I can change its 
resolution by pressing the Select All button at the top of the 
Multiscale dialog, then change the Resolution value in the middle of 
that dialog and press Resurface. A resolution value of 0 will make very 
high resolution solvent excluded molecular surfaces. The lighting 
effects will look better on lower resolution surfaces (e.g. 5 Angstroms).

I've attached an example image.


Darrell Hurt wrote:
> I may have to use the Multiscale Coloring command tool that is not 
> distributed with Chimera as documented here:
> http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html
> This seems to work well.
> Darrell
> ------------------------------------------------------------------------
> *From: *Darrell Hurt <darrellh at niaid.nih.gov>
> *Date: *Wed, 20 Aug 2008 10:46:16 -0400
> *To: *<chimera-users at cgl.ucsf.edu>
> *Conversation: *MultiScale.color_surfaces_to_match_atoms() and 
> MultiScale mesh resolution ???
> *Subject: *MultiScale.color_surfaces_to_match_atoms() and MultiScale 
> mesh resolution ???
> Hi there,
> I’m trying to use the command 
> MultiScale.color_surfaces_to_match_atoms(). I want to point out a 
> mutation on the surface of a virus. I can color the atoms correctly, 
> but I can’t figure out how to apply that color to the MultiScale 
> low-resolution surface. Any hints on how to use this command?
> Also, how can I increase the mesh resolution on MultiScale surfaces 
> for input for 3D printing?
> Thanks!
> Darrell

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