Hi Gianluca, You get the sphere with stick_ball=on. It's unexpected that batch mode and GUI mode give different results. Could it be that you have the stick_ball setting in a (directory specific) pymolrc file, and/or do you pass -k flag (ignores pymolrc files) in batch mode?
Cheers, Thomas > On Jul 2, 2017, at 5:32 PM, Gianluca Tomasello <giagi...@gmail.com> wrote: > > Hi, I am trying to execute a script that sets valence bonding on sticks and > then it gives me back a rendered image. There seems there is a difference > when i try to run the script normally or in batch mode (pymol -cq script.py). > If i run it in batch mode, each atom with a double bond is rendered without > the sphere in the atom center (only double bond is shown). > > Instead, if i try to execute the script in default mode the central atom > sphere is correctly rendered. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
