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 GUI.

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.