Hello, I am doing some epitope analysis and I am generating images of each potential epitope overlaid and colored on the antigen model. I have a script that loops through a list of residue sets (epitopes) and uses chimera to generate the images. The script works if I call it from within Chimera running on Mac OSX. I just installed the headless version on Redhat linux and was trying to modify my python script to run on the headless version and I ran into a few issues I would like some advice with. 1. Say I have ten sets of residues, which should produce 10 images. I get the first one, but then I get the following error: Traceback (most recent call last): File "/opt/bin/Chimera64-1.6.2rc/share/chimeraInit.py", line 686, in init midas_text.doRunScript("runscript", script) File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 2037, in doRunScript execfile(scriptPath, scriptGlobals) File "batchEpitopeModel3.py", line 144, in <module> callChimera(data[ab][4],data[ab][5],fn,dn) File "batchEpitopeModel3.py", line 29, in callChimera rc("open " + trimer) File "/opt/bin/Chimera64-1.6.2rc/share/chimera/__init__.py", line 2426, in runCommand makeCommand(*args, **kw) File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 1427, in doOpen modelArg, noprefs) File "<string>", line 1, in <module> File "/opt/bin/Chimera64-1.6.2rc/share/Midas/__init__.py", line 1937, in open raise MidasError('%s' % msg) MidasError: No such file or directory Error while processing 'batchEpitopeModel3.py': MidasError: No such file or directory File "/opt/bin/Chimera64-1.6.2rc/share/Midas/__init__.py", line 1937, in open raise MidasError('%s' % msg) It seems like Chimera terminated my script, even though it should be executing a loop. 2. The images that are generated on the Mac are large, hi-res pngs, but the images generated by the headless version are very small, low-res versions. I am not setting any image dimensions, are the defaults different between the two versions? Thanks for any help. I can post (or email directly) part of my python code if that is helpful. -Mark -This e-mail and any attachments may contain CONFIDENTIAL information, including PROTECTED HEALTH INFORMATION. If you are not the intended recipient, any use or disclosure of this information is STRICTLY PROHIBITED; you are requested to delete this e-mail and any attachments, notify the sender immediately, and notify the LabCorp Privacy Officer at privacyofficer@labcorp.com or call (877) 23-HIPAA / (877) 234-4722.