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

[Darrell Hurt]

Thank you. The answers from Elaine Meng and Tom Goddard are definitely what
I was looking for.

Darrell

-- 
NIH Researchers: check out our new web site
<http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx>
 
Darrell Hurt, Ph.D.
Section Head, Biocomputing Research Consulting
Bioinformatics and Scientific IT Program (BSIP)
NIAID Office of Technology Information Systems (OTIS)
National Institutes of Health, DHHS
Contractor, Lockheed Martin

4 Memorial Drive, Room 424
Bethesda, MD 20892-0485
Mobile: (301) 758-3559
Fax: (301) 402-0366
NIAID Intranet: http://bioinformatics.niaid.nih.gov
<http://bioinformatics.niaid.nih.gov/>

Disclaimer:
The information in this e-mail and any of its attachments is confidential
and may contain sensitive information. It should not be used by anyone who
is not the original intended recipient. If you have received this e-mail in
error please inform the sender and delete it from your mailbox or any other
storage devices. National Institute of Allergy and Infectious Diseases shall
not accept liability for any statements made that are sender's own and not
expressly made on behalf of the NIAID by one of its representatives.



From: Tom Goddard <goddard at cgl.ucsf.edu>
Date: Wed, 20 Aug 2008 12:17:22 -0400
To: "Hurt, Darrell (NIH/NIAID) [C]" <darrellh at niaid.nih.gov>
Cc: <chimera-users at cgl.ucsf.edu>
Conversation: [Chimera-users] MultiScale.color_surfaces_to_match_atoms() and
MultiScale mesh resolution ???
Subject: Re: [Chimera-users] MultiScale.color_surfaces_to_match_atoms() and
MultiScale mesh resolution ???

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.

Tom


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,
>
> I¹m 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 can¹t 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
>



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080820/dd74150f/attachment.html>