<div dir="ltr">Hi Elaine, <div>Thank you very much for the reply. It works now. I figured that I was using an incorrect filename. I should have used xxx.cxc.</div><div><br></div><div>Shanti Pal</div><div><br></div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div> </div><div><br></div><div><br><br></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 30 Mar 2022 at 16:17, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Shanti,<br>
Yes, you can run a script by simply opening the script file, as long as the commands or code in it are written correctly for that program. If you are trying to write a script with commands but you are not very experienced with the program, you should first test the commands interactively (by entering them into the command line) in the graphical user interface of the program to make sure they are correct.<br>
<br>
Some other tips <br>
- a command script should be a plain text file<br>
- Chimera and ChimeraX are two different programs; a script for one will not work in the other<br>
- make sure you have a reasonably new version of the program (P.S. there is also a <a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a> mailing list if you want to ask specifically about ChimeraX)<br>
- if you want help when something doesn't work, you will need to describe exactly what you did and what happened, and possibly also include your structure data ... "does not work" is not enough information<br>
<br>
If Chimera, then you need Chimera commands. Usually filename ends in .cmd or .com<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html</a>><br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile</a>><br>
<br>
If ChimeraX, then you need ChimeraX commands. Usually filename ends in .cxc<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands</a>><br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files</a>><br>
<br>
For either program, you could also write scripts in python code, or save and restore session files, but again, a script or session for Chimera would only work in Chimera, and one for ChimeraX would only work in ChimeraX.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Mar 30, 2022, at 5:00 PM, Shanti Pal Gangwar via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi<br>
> I am trying to run a script in chimeraX but it did not work. I even downloaded the example files and that also did not work. I wonder if a script can be run in ChimeraX as we do in PyMol.<br>
> Any help would be appreciated.<br>
> Thank you<br>
> Shanti Pal<br>
<br>
</blockquote></div>