Hi Chaava, You need to split the multi-state assembly into separate single-state objects. Then run APBS on a selection which includes all these objects. This is a huge system for APBS, you probably need to increase the grid spacing, otherwise it will take forever or might fail (PyMOL automatically retries several times with increased grid spacing if APBS runs out of memory).
Here is an example I successfully ran on my MacBook with PyMOL 2.1: # download assembly (multi-state object) set assembly, 1 fetch 3j7l, async=0 # split states into individual objects split_states 3j7l delete 3j7l In the GUI: - Open "Plugin > APBS Electrostatics" - Selection: polymer & 3j7l_* - Calculate Map with APBS > Options >> Grid Spacing: 2.0 (or larger) - Run Took about 20min to compute. Hope that helps. Cheers, Thomas > On Jul 5, 2018, at 1:21 AM, Chaava CA <chaav...@gmail.com> wrote: > > Hello, > > I am very new to pymol and mainly use it for visualizing proteins and surface > properties. I am trying to generate the electrostatic potential map of a > Adeno associated viral particle which has 60 identical subunits. I have the > PDB file for it but it only shows 1 subunit at a time. In addition when I > generate the pqr I only get the potentials for one subunit. How can I > generate the potential for the entire viral particle and visualize it? I do > have the APBS plugin. > > If someone can explain this process in slightly more layman’s terms and > stepwise approach it would be very helpful. > > Any help is much appreciated. > > Thank you! -- 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
