[apbs-users] ball surface vs flat surface

[sacha uljon]

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]

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

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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