Re: [apbs-users] visualization in PyMol
Biomolecular electrostatics software
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From: Thomas H. <tho...@sc...> - 2015-08-19 16:26:18
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Hi Wolfram, Yes that's the correct way of doing it. Just add: 4) set surface_ramp_above_mode See: http://pymolwiki.org/index.php/Surface_ramp_above_mode Cheers, Thomas On 19 Aug 2015, at 11:45, wtempel <wt...@GM...> wrote: > Hello, > I would like to compare the the electric surface potentials of releated proteins, without using the PyMOL APBS plugin. > To this end, I have used pdb2pqr and apbs to to produce “pqr” and “dx” files and loaded the files as objects “pqr” and “dx”, respectively. > Is it an abuse of the calculations’ results if I > 1) show surface pqr > 2) ramp_new ramp, dx, [-10,0,10] > 3) set surface_color, ramp, pqr > to show (and compare) surface potentials for inference of binding selectivity toward peptides, nucleotides, etc.? > Is my method correct, as in: can I expect to see the correct APBS potentials on the PyMOL-generated surface, for that given surface? > If so, is the PyMOL-generated surface over the pqr coordinates a reasonable choice for my purpose? > Thank you, > Wolfram Tempel -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |