[Chimera-users] using old cmd files in chimerax

[Elaine Meng]

Hi Bryan,
If I understand correctly, by "old" you mean works in Chimera... and would like to know how to get to the same end results except in ChimeraX, so I also CC'd chimerax-users at cgl.ucsf.edu.

Since ChimeraX and Chimera commands do have differences, you cannot simply open Chimera command files in ChimeraX.

Possible routes to getting what you want:

(1) text-edit the cmd file to change Chimera commands to ChimeraX commands, change the filename suffix of that plain-text file to .cxc and then open it in ChimeraX.  ChimeraX does have the capability to read ResMap maps and then use the values to color a surface, so this is a viable route.  The downside is that it requires knowing or looking up the differences in the commands.  Many commands are highly similar so it wouldn't necessarily be as bad as it sounds, however.  You can open both the original map and the ResMap map files with ChimeraX command "open", control which is shown as a surface with the ChimeraX Volume Viewer tool or "volume" command, and color the surface by the values of the other map using "color sample".  See ChimeraX User Guide:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>

(2) or simply dispense with trying to use a command script and instead use ChimeraX tools and/or commands interactively.  You can use ChimeraX menu: File... Open to open the maps (aka volume data), and there is a Surface Color tool (same function as "color sample" command):
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html>

(3) in the more general case of Chimera command scripts involving atomic data, you can open/run the script in Chimera, export a session from Chimera as a ChimeraX python file (Chimera menu: File... Export Scene or Chimera command "export") and then open that file in ChimeraX to regenerate the session contents.  
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>

However, this Chimera->ChimeraX export feature does not (yet) cover maps, map isosurfaces, and a few other things.

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


> On Mar 28, 2022, at 12:01 PM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> How do I used/open old cmd scripts I have or outputs from things like resmap in chimerax?
>