[chimerax-users] cropping map to red part

[Elaine Meng]

Hi Tianming,
You didn't say what your coloring means: whether it is color by distance or some property.  However, you can get parts of a map by various different methods:

(1) volume zone (hide some parts by some distance from some atoms)
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone>

(2) interactively using the Map Eraser tool to set some parts to zero
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#erase>

(2) interactively cropping the map box, e.g. in Volume Viewer choosing display style "box" and using the mouse to "crop volume"
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>

I prefer to avoid zooming -- there are so many users and so many questions it would be too many meetings!
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 21, 2022, at 6:32 AM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX group,
>  
> My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins.
> I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result:
> <image001.png>
>  
> I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want.
>  
> Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help.
>  
> Best,
> Tianming