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.