Re: [Jmol-users] Fwd: obj surface files exported from pymol

[Robert H. <ha...@st...>]

On Fri, Nov 26, 2010 at 9:36 AM, Alexander Rose <ale...@we...
> wrote:

>
> > form of
> >
> > isosurface select {protein} ignore {not protein} sasurface 0
> >
> > But they aren't exactly that, either, so perhaps PyMOL is adding
> > hydrogen atoms first, then doing the calculation?
>
> > that is, a surface at the van der waals radius that is a rounded out
> no, definitely not
>
>
>

Checking this further, PyMOL's surface is similar to Jmol's

set defaultVdw BABEL
isosurface solvent 1.4

That said, in compariing these, I did find Jmol's molecular/solvent surface
somewhat disappointing. I've added the following:

isosurface solvent 1.4 FULL

meaning "Do a full analysis," but this can take quite some time. I'd really
like to know how PyMOL creates that surface so fast.



> > I have no idea how PyMOL creates the troughs for the molecular
> > surfaces. Anyway, it's not a typical solvent-accessible surface, which
> > would be considerably larger.
>
> I did not thought much about it when I named my file with 'sas' for
> solvent-accessible surface, sorry for the confusion
>
>
yes, it's a solvent-excluded surface, not what is pointed to by the PyMOL
Wiki, which is a solvent-accessible surface.


>
> > What's the PyMOL command that gives this?
> > I guess you showed me the PyMOL command -- show surface.
> >
> > http://www.pymolwiki.org/index.php/Surface says that's the Connolly
> surface. I don't believe it, though. It's too rounded. It must be a
> molecular surface with troughs.
> > Actually, I think the troughs are a bit better than Jmol's. Jmol's are a
> bit deep.
>
> you guessed right, it's
>
> PyMOL> show surface
> with the default solvent radius of 1.4 A
>
> it looks to me like the solvent-excluded surface ( = Connolly surface ???)
>
> right, solvent-excluded.


>
> PyMOL> set surface_solvent, 1
> PyMOL> set solvent_radius, 1.4
>
> this is the solvent-accessible surface
>
>
ah, interesting

>
> I'll look some more into it when I have time and report back.
>
>
great. Now that we can do these comparisons, you will be telling me how
Jmol's surfaces need improvement. I've spent all weekend working on this
trying different ideas, and I don't have a good solution. But I did learn a
lot about solvent-excluded surfaces. Very interesting how they can have
discontinuities.



>
> Alex
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900