[chimerax-users] Help with Zone features

[Binh Nguyen]

Dear Elaine,

Thanks for the instructions. This is what I got, but the map density edge is not as sharp compared to the reference figure (my first email). Is there anything else that I can improve?

[cid:c5fc944f-33ff-425a-9454-3c0510e9e67d]

Thank you so much,

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: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, August 30, 2022 3:25 PM
To: Binh Nguyen <AnBinh.Nguyen at UTSouthwestern.edu>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Help with Zone features

EXTERNAL MAIL

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

CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

________________________________

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Medical Center

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