Re: [apbs-users] ball surface vs flat surface
Biomolecular electrostatics software
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From: Thomas H. <tho...@sc...> - 2015-10-06 14:05:40
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Hi Sacha, In the PyMOL APBS Plugin, when showing "Molecular Surface", you should set: [ ] Solvent accessible surface [x] Color by potential on sol. acc. surf. These checkboxes control two settings, see: http://wiki.pymol.org/index.php/surface_ramp_above_mode Hope that helps. Cheers, Thomas On 05 Oct 2015, at 15:24, sacha uljon <sac...@gm...> wrote: > Hello, > I am trying to make a figure of a protein and a peptide ligand. Using the default settings, the protein surface has a ping-pong ball like texture that makes the ligand hard to see. Others have used the .pymol generate>vacuum potential command to get a flatter surface where the ligand/peptide can be more easily seen. (sort of "pops out") How is this done in APS? I have tried randomly adjusting variables, but surprisingly that did not help. > I am using the .pymol plug in-- which variable do I change? Thanks in advance, > Sacha -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |