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<TITLE>Re: [Chimera-users] MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???</TITLE>
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<FONT FACE="Arial"><SPAN STYLE='font-size:12.0px'>Thank you. The answers from Elaine Meng and Tom Goddard are definitely what I was looking for.<BR>
<BR>
Darrell<BR>
<BR>
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<HR ALIGN=CENTER SIZE="3" WIDTH="95%"><B>From: </B>Tom Goddard <goddard@cgl.ucsf.edu><BR>
<B>Date: </B>Wed, 20 Aug 2008 12:17:22 -0400<BR>
<B>To: </B>"Hurt, Darrell (NIH/NIAID) [C]" <darrellh@niaid.nih.gov><BR>
<B>Cc: </B><chimera-users@cgl.ucsf.edu><BR>
<B>Conversation: </B>[Chimera-users] MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???<BR>
<B>Subject: </B>Re: [Chimera-users] MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???<BR>
<BR>
Hi Darrell,<BR>
<BR>
You need to use the multiscale coloring command "msc". Here's an example<BR>
using Chimera commands (Favorites / Command Line):<BR>
<BR>
open viperID:1p58<BR>
color blue :86.A<BR>
msc #1 :86.A 15<BR>
<BR>
The first command opens a dengue virus model from the VIPERdb database.<BR>
Then I color residue 86 of chain A blue. That just colors the atoms of<BR>
the residue not the surface. Then the msc command colors the multiscale<BR>
surfaces (model identifier #1 seen in Favorites / Model Panel) making<BR>
the surface color match the blue of residue 86 within 15 Angstroms of<BR>
that residue.<BR>
<BR>
After I open the model and before coloring it I can change its<BR>
resolution by pressing the Select All button at the top of the<BR>
Multiscale dialog, then change the Resolution value in the middle of<BR>
that dialog and press Resurface. A resolution value of 0 will make very<BR>
high resolution solvent excluded molecular surfaces. The lighting<BR>
effects will look better on lower resolution surfaces (e.g. 5 Angstroms).<BR>
<BR>
I've attached an example image.<BR>
<BR>
Tom<BR>
<BR>
<BR>
Darrell Hurt wrote:<BR>
> I may have to use the Multiscale Coloring command tool that is not<BR>
> distributed with Chimera as documented here:<BR>
><BR>
> <a href="http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html">http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html</a><BR>
><BR>
> This seems to work well.<BR>
><BR>
> Darrell<BR>
><BR>
><BR>
> ------------------------------------------------------------------------<BR>
> *From: *Darrell Hurt <darrellh@niaid.nih.gov><BR>
> *Date: *Wed, 20 Aug 2008 10:46:16 -0400<BR>
> *To: *<chimera-users@cgl.ucsf.edu><BR>
> *Conversation: *MultiScale.color_surfaces_to_match_atoms() and<BR>
> MultiScale mesh resolution ???<BR>
> *Subject: *MultiScale.color_surfaces_to_match_atoms() and MultiScale<BR>
> mesh resolution ???<BR>
><BR>
> Hi there,<BR>
><BR>
> I’m trying to use the command<BR>
> MultiScale.color_surfaces_to_match_atoms(). I want to point out a<BR>
> mutation on the surface of a virus. I can color the atoms correctly,<BR>
> but I can’t figure out how to apply that color to the MultiScale<BR>
> low-resolution surface. Any hints on how to use this command?<BR>
><BR>
> Also, how can I increase the mesh resolution on MultiScale surfaces<BR>
> for input for 3D printing?<BR>
><BR>
> Thanks!<BR>
><BR>
> Darrell<BR>
><BR>
<BR>
<BR>
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