[Chimera-users] chimera --nogui --script option not doing anything!

Ahir Pushpanath ahir29 at gmail.com
Tue Nov 27 08:03:21 PST 2018

Dear Chimera crew,
                     I am having serious trouble running my script using
chimera --nogui --script option. I tried running a simple script that just
prints a comment, and i dont get anything returned on the cmd, let alone
the actual script.

The cmd does not flag up any errors , it just does nothing and return back
to the prompt.
I have chimera 1.13.1 and its added to the system path - "C:\Program
Files\Chimera 1.13.1rc\bin\". I can launch chimera fine from the command
line showing its added to path fine.

I am completely stumped! Also, the script works fine within the IDLE of the

See code below:

import os
> print "Script is running"
> from chimera import runCommand as rc # use 'rc' as shorthand for runCommand
> from chimera import replyobj # for emitting status messages
> # change to folder with data files
> os.chdir("C:/Users/JM/Documents/Public Qsync/Jenny
> Taylor/IREDs/Structures/")
> # gather the names of .pdb files in the folder
> file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")]
> # loop through the files, opening, processing, and closing each in turn
> for fn in file_names:
>         res = "tyr"
>         if fn == ""2NAD.pdb":
>                 print fn
>                 replyobj.status("Processing " + fn) # show what file we're
> working on
>                 rc("open " + fn)
>                 for b in range(1,300):
>                         rc("sel #0" + ":"+str(b))
>                         rc ("swapaa "+res + " sel criteria p")
>                         rc ('write format pdb #0'+ " " + fn
> +"_"+res+'mutated.pdb')
>         rc("close all")
> # uncommenting the line below will cause Chimera to exit when the script
> is done
> rc("stop now")

Dr. Ahir Pushpanath* PhD.*
Senior Biologist,
Johnson Matthey.
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