[chimerax-users] Command use

[Elaine Meng]

Dear Wojciech Witek,
It will be easier once you understand how to interpret the command help.  "surfaceSmoothing" and "squareMesh" are not commands themselves, but options of the "volume" command.  So just like your command

volume #2 style mesh

... it would be something like

volume #2 squareMesh true

See the "volume" command surface and mesh options, where the "Usage" at the top shows the general form of the main command, and below it the specific options are listed:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf>

It will be similar for the other options you mentioned, they need to be given as part of their respective main commands (which will have some "Usage" line in the upper parts of the same pages in which these options appear, e.g. "lighting" is the main command for depthcue options, "ribbon style" for ribbon style options).  

There is no option to change mesh linewidth, however.

As for the color including transparency, although you could use commands, the easier GUI way is to simply click the color well, the green square to the left of "#2" and right above the histogram in the Volume Viewer tool.  That will open your system color editor dialog in which you can change the color, including adding transparency.

This is a publicly available email forum, so in the future, please do not send information that needs to be kept confidential.  We will work on removing the previous message, or at least the image within it, from the archive.

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 19, 2023, at 7:00 AM, Wojciech Witek via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX Team, 
> 
> I am trying to change this mesh properites because it covers the ligand too much (attachment). I wanted to make the lines thinner or transparent or divided in different ways. I could not find anything in the GUI so I searched for commands but apparently I use them wrong. Could you please guide me on how to use commands, let's say like this one : surfaceSmoothing true | false? If I type "true", I see an error in the log file. Where can I find what arguments should be use with a specific function?I had the same struggle with depth cueing, ribbon style edition and many other functions.
> 
> ChimeraX is a great software but using GUI is so much easier to get familiar with, learn and utilize changes, comparing to command line. 
> 
> See attached file containing ligand, mesh and a log full of errors from pasted commands. Please, keep it confident because it is unpublished yet.
> 
> Regards, 
> Wojciech Witek