Re: [PyMOL] Surface and SASA

[Alan W. S. da S. <al...@bi...>]

Hi Dr. Warren!

=09I know about MSMS license.  Indeed, I'm suggesting an approach
similar to what VMD did, i.e., it can link, run and catch results to plot,
all that as a option conditioned to one gets or not MSMS installed,
separately, in one's machine.

=09Sanner had done and released a binary program to visualise MSMS
data only for SGI.  But he stopped it.  So, I wonder that PyMol may
replace it without difficult and with a lot of advantages.

=09Hence, as far as I concern, it does not matter what License MSMS
features, since PyMol would take care only of MSMS' data output.

=09I know a little bit about Connoly code but it suffers the same
license problem.

=09I steadily support GNU directions and I believe that it will not
uncharacterise your beautiful program.

Sincerely,

On Mon, 10 Feb 2003, Warren L. DeLano wrote:

>
> Alan,
>
> Last I checked, MSMS was saddled with a number of constraints on its usag=
e
> and redistribution.  Though source code can be obtained under certain
> conditions, MSMS doesn't meet the minimal "open-source" software
> requirements that would make it eligible for inclusion into PyMOL.  I
> talked with Michel Sanner about this a couple years ago, but he didn't
> think there was much that could be done. (DISCLAIMER:  I haven't
> double-checked this since -- so things may have changed since without my
> knowledge).
>
> The other problem with MSMS is that it bombs with large or convoluted
> structures on machines which don't have enough stack space.  Plus, I
> believe it is written in C++.  PyMOL current only depends on C and
> Python, and am I loathe to introduce a new language dependency without a
> compelling reason.
>
> Though it is a matter of personal preference, some of us actually prefer
> the appearangce of surfaces created by PyMOL and Grasp over those created
> by MSMS or Insight, which have characteristic "streaks".  No question
> PyMOL is slower to calculate surfaces though.  The algorithm was created
> in a single weekend and is very inefficient.  I've spent considerable tim=
e
> trying to optimize it since, but have only been able to boost performance
> by about 10-30%.  I think the order of this naive, brute-force algorithm
> is just too high.
>
> If someone can find a better open-source surface calculation code, I'd be
> happy to include it in PyMOL as an option.  The only catches: it must be
> written in C, and it must be available under a BSD-style open-source
> license (free for commercial use, with no limits on redistribution).
>
> Anyway, approximate partial surface areas can be obtained in PyMOL using
> the dot representation, but that isn't yet documented...

-----------------------
Alan Wilter S. da Silva
-----------------------
 Laborat=F3rio de F=EDsica Biol=F3gica
  Instituto de Biof=EDsica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil