Hi Dr. Elaine,

I tried the way you suggested, it is helpful. One more question is that, the one I am trying to work on now, the colored map, is a density map read from .dx file. Is there any way I can save the edited map (aftering cropping and erasing) as a new .dx file?

Best,

Tianming

发件人: Elaine Meng <meng@cgl.ucsf.edu>
日期: 星期三, 2022年9月21日 上午11:12
收件人: Tianming Qu <tqu@fsu.edu>
抄送: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
主题: cropping map to red part

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://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html*zone__;Iw!!PhOWcWs!0DKqwfdTFNswYzmNztpdwEHNL-g-Xq9RRb3z0J8PDSjtr2PqTq7LtJUyLwvp8-ms7JBh4ttYW3lG7A$  >

(2) interactively using the Map Eraser tool to set some parts to zero
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html__;!!PhOWcWs!0DKqwfdTFNswYzmNztpdwEHNL-g-Xq9RRb3z0J8PDSjtr2PqTq7LtJUyLwvp8-ms7JBh4tvUR5JHYw$  >
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html*erase__;Iw!!PhOWcWs!0DKqwfdTFNswYzmNztpdwEHNL-g-Xq9RRb3z0J8PDSjtr2PqTq7LtJUyLwvp8-ms7JBh4tuz8_GQpg$  >

(2) interactively cropping the map box, e.g. in Volume Viewer choosing display style "box" and using the mouse to "crop volume"
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html__;!!PhOWcWs!0DKqwfdTFNswYzmNztpdwEHNL-g-Xq9RRb3z0J8PDSjtr2PqTq7LtJUyLwvp8-ms7JBh4ttEG0MYpA$  >

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@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