Thanks for the so quick reply Dr. Elaine.

One more question, can chimera calculate the volume of voxels for density map?

Best,

Tianming

发件人: Elaine Meng <meng@cgl.ucsf.edu>
日期: 星期三, 2022年9月21日 下午3:09
收件人: Tianming Qu <tqu@fsu.edu>
抄送: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
主题: Re: [chimerax-users] cropping map to red part

Hi Tianming,
Sorry no, ChimeraX can save maps (volume data) in several formats, but not .dx

You can use command "save formats" to list the possible formats in the Log, or see the list at our website here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html*mapformats__;Iw!!PhOWcWs!1Y4X9rQfuEq8ZsOGcet7K95FdmjdltcLZcBMIhDzXCBX6m4QcWQzl_U1ZuinD0kYIi8i19J92G-9rQ$  >

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 11:52 AM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> 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