Re: [PyMOL] refinement in morph

Hi Jianghai, you need to fix the jumping atoms before doing the refinement. Lets say you want to fix all chloride ions, it would look like this: # morph without refinement rigimol.morph(rin, rout, refinement=0, async=0) # get rid of the default movie cmd.mstop() cmd.frame(1) cmd.mset() # fix

Re: [PyMOL] running pse file in batch mode

Hi Jon, there is no need to convert the pse file into a script, just write a short script which loads the pse file in the beginning. load session.pse scene 001, recall viewport 800, 600 png scene001.png, ray=1 You can run that in batch mode. Cheers, Thomas On Mar 6, 2013, at 4:11 PM,