On Fri, Nov 26, 2010 at 9:36 AM, Alexander Rose <alexander.rose@weirdbyte.de> 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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