[chimerax-users] Help with Zone features

[Tom Goddard]

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



> On Aug 30, 2022, at 1:25 PM, Elaine Meng via ChimeraX-users <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> 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
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220830/6902f95a/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 6y1a.png
Type: image/png
Size: 675601 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220830/6902f95a/attachment-0001.png>