[chimerax-users] Help with Zone features

[Guillaume Gaullier]

It looks like the example image Binh provided also used either `lighting flat` or `lighting soft`. At least I get something a bit closer to the example image when I rerun Tom’s example and add either of these lighting commands.
Cheers,

Guillaume


> On 30 Aug 2022, at 22:49, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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
> 
> <6y1a.png>
> 
>> 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 <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 <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 <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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> 
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