[chimerax-users] Help with Zone features

[Binh Nguyen]

Dear Tom,

Thank you so much. It looks perfect. and Yes, a layer from our Amyloid.

Best,

B


_____________________________________________
Binh A. Nguyen, Ph.D.
@ Saelices's Lab
Center for Alzheimer’s and Neurodegenerative Diseases

Peter O’Donnell Jr. Brain Institute

UT Southwestern Medical Center


________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Tuesday, August 30, 2022 3:49 PM
To: Binh Nguyen <AnBinh.Nguyen at UTSouthwestern.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Help with Zone features


EXTERNAL MAIL

Hi Binh,

  Looks like an image of one plane of a an amyloid fibril.  Here are example commands that make the attached image.

open 6y1a
hide ~/A,B
style stick
color byhet
open 10669 from emdb
vol zone #2 near /A,B range 3 new true
volume #3 color gray transp 0.8 level 4
set bgcolor white
graphics silhouette true

   Tom

[cid:87179850-7B9F-4EE5-8FD8-9BE5409E5318]

On Aug 30, 2022, at 1:25 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Dear Binh,
It looks more like an electron density map (not solvent-accessible surface).  So you would need to open an atomic structure and open its electron density map, and show the structure as sticks and the map as a mesh.  For example commands, see the Quick Start Guide, scroll down to the next-to-the last section that shows 1a0m and its density map.  This includes a "vol zone" command.

<https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html>

Or if you are using the GUI interactively you can adjust the map style (e.g. mesh or not) and level using the Volume Viewer tool, which automatically appears when you open a density map file.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>

If you want a similar thing but only with molecular surface, not density map, then you don't need zone.  You can just show the surface for whatever parts you want by specifying in a command or selecting.  E.g.

open 1gcn
hide ribbons
show atoms
surface :1-8
surface style mesh

...or you could make surface transparent...

transparency 50
surface style solid

Details of all of the commands are in the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>

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

On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Dear ChimeraX developers,

Would you please show me how to make this following figure?
<image.png>

I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it.
Any hint is much appreciated.

Warm regards,

B


_____________________________________________
Binh A. Nguyen, Ph.D.
@ Saelices's Lab
Center for Alzheimer’s and Neurodegenerative Diseases
Peter O’Donnell Jr. Brain Institute
UT Southwestern Medical Center


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