[chimerax-users] Surface dust command in the .cxc script

[Elaine Meng]

Hi Ze,
You should always try the commands by typing into the command line before putting them in the .cxc file.  It should work exactly the same in the cxc file as in the command line.

My guess is that the issue is not the cxc file, but that the command is either used incorrectly or there is a misunderstanding about how it works.  We use "dust" to mean separate enclosed blobs, usually from contouring a density map.  If you are showing atomic patches in a single molecular surface that only look separate because parts of the surface are hidden, that is a different matter.

There are two cases of these atomic patches,

(1) from using "surface zone" ... in that case you probably need to include the "max" (maxComponents) option of "surface zone":
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#zone>

There is an example of that in the Protein-Ligand Binding Sites tutorial:
<http://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#mlp>

(2) from using "surface" with only certain atoms specified... in that case you may want to also use the "visiblePatches" option:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options>

When you ask a question, it is important to give more information about what you are trying to do and what you did, such as exactly what commands were typed or in the script, and whether you got an error message. Just saying something didn't work leaves too many different possibilities.  When you think it is a bug, you can use menu: Help... Report a Bug.  However, I'm guessing this time it is not a bug.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 1, 2020, at 7:30 PM, 李 泽 <li-ze at hotmail.com> wrote:
> 
> Hi all:
> I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all.
> Best,
> Ze
>