[chimerax-users] How to open .py file downloaded from MOLEonline in ChimeraX?

[Elaine Meng]

Hi Kate,
Yes, the MOLEonline scripts are written just for Chimera. ChimeraX is a different program and won't work with Chimera sessions or python scripts written for Chimera.  

Chimera does have an option to export a file for input to ChimeraX, but it only includes the atomic/ribbon displays, not yet surfaces (but see below, to my surprise it worked!).  If the reason for using ChimeraX is display only (not calculations requiring atomic data), other Chimera export formats may also work, like Collada.  ChimeraX can read Collada files.

See Chimera menu: File... Export Scene, options include ChimeraX and collada:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
... or Chimera's "export" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>

Just now I tested exporting a Chimera scene showing MOLEonline results (Chimera 1.16 daily build from August was what I had handy) and even though I got a warning message that the export to ChimeraX file does not work for surfaces, to my surprise, when I open it in ChimeraX, voila!  It does include the tunnel displays!  So maybe it WILL work for your situation. You may have to change the background color yourself.  I was also able to export collada (.dae) file from Chimera that gave the same display when opened in ChimeraX. The ChimeraX choice is better than collada, since it will also include all the other tunnels that aren't displayed when you export, see screenshot below:

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

How it looked in Chimera when I exported a file for ChimeraX


How it looks in ChimeraX after I open that file (except I had to change background to white again myself), can hide/show all the tunnels. 



> On Oct 29, 2021, at 7:37 PM, Kate Kim via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello, 
> I've been using Chimera in the past for opening downloaded .py files from MOLEonline to visualize tunnels in my structure. When I try to do the same in ChimeraX, I get the following error:
> 
> Traceback (most recent call last):
> File "/Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py", line 1, in <module>
> import chimera, _surface, numpy
> ModuleNotFoundError: No module named 'chimera'
> 
> Error opening python file /Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py
> toolshed show
> 
> Any suggestions on the best approach to visualize MOLE channels using ChimeraX?
> 
> Thank you,
> Kate
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