Hello again dear mates! I've been working those days in my extension and the GUI es almost finished. Now I want to fill this skeleton with the process logic. To understand between us, I have an external compiled program that is executed in shell this way: ./bin/myProgram ./dir1/pdbselected.pdb ./dir/mapselected.ccp4 arg3 arg3 arg4 And for sure, in my .py test, it has to be executed as: import subprocess subprocess.call(["./Users/Solar/Desktop/parent/child1/child2/bin/myProgram", "/Users/Solar/Desktop/parent/child1/child2/dir1/pdbselected.pdb", "/Users/Solar/Desktop/parent/child1/child2/dir1/mapselected.ccp4", "arg3", "arg4", "arg5"]) The problem is to execute this in Chimera as an extension. The coding I made for the PDB and the Map it's similar to the FitMap tool (in Volume Data), where I use: ... # PDB from chimera import Molecule mlist = [m for m in fit_object_models() if isinstance(m, Molecule)] fstart = mlist[0] if mlist else None from chimera.widgets import ModelOptionMenu om = ModelOptionMenu(ff, labelpos = 'w', label_text = 'Fit ', initialitem = fstart, listFunc = fit_object_models, sortFunc = compare_fit_objects, command = self.object_chosen_cb) om.grid(row = 0, column = 0, sticky = 'w') self.object_menu = om # Map fm = Volume_Menu(ff, ' in map ') fm.frame.grid(row = 0, column = 1, sticky = 'w') self.map_menu = fm -- The question is, how can I pass the PDB to the compiled program as it is expected? Or, another possible solution, the paths of the PDB and the Map loaded in Chimera? I didn't found any friendly doc (methods, info and so on) about this and and I'm a mess :/ Thank you in advance dear coworkers! Pablo