Just as a matter of general philosophy: PyMOL is primarily intended as a
display program and communications program, with (admittedly) rather limited
emphasis placed on rigorous analysis and generation of quantitative
information. There's only so much time in the day, so we have to choose our
battles and set our priorities.
The ongoing vision for core PyMOL is that remain firmly anchored the
visualization realm while leveraging Python to easily link out to rigorous
tools that specialize in various forms of number-crunching and analysis --
written by teams of people who make rigor their top priority. Examples
include GROMACS, MMTK, APBS, Rosetta, Modeller, DSSP, MSMS, PHENIX, CCP4,
Maestro, MOE, Discovery Studio, and so on.
DeLano Scientific LLC
Subscriber Support Services
"Not yet a PyMOL Subscriber, but want to support the project? Email
sales@... to quote your lab, school, or employer. Thank you for
sponsoring this open-source endeavor!" -WLD
> -----Original Message-----
> From: pymol-users-bounces@...
> [mailto:pymol-users-bounces@...] On Behalf Of JJ
> Sent: Thursday, November 22, 2007 10:43 PM
> To: pymol-users@...
> Subject: Re: [PyMOL] obtaining coordinates of solvent-surface points
> From: Robert Campbell <robert.campbell@......> -
> 2007-11-22 21:56
> Rather than use PyMOL's surface, I've used the triangulated
> surface output by Michel Sanner's msms program. <<
> Thanks much Rob. Can you please tell me why it might be
> better to use msms to calculate surface points rather than
> the pymol algorithm. Are there advantages to one or the other?
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