RE: [PyMOL] Question about surface calculation

[Warren D. <wa...@de...>]

Fred,

I think Lieven answered the second part, so I'll answer the first:

PyMOL's surfaces are discrete approximations of the solvent contact surface
(the surface of waters in contact with the protein at all possible
positions).  

I generally think of the "solvent accessible surface" as being the surface
carved out by the center of those same waters.  PyMOL doesn't currently
provide a solid representation of this surface, but you can show it using
dots:

set dot_solvent,1
set dot_density,3
show dots

In theory, mesh_solvent should do the same thing for mesh surfaces, but I
just found a major bug in that code -- so don't use "mesh_solvent" until
after the next release...

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Fred Berkovitch
> Sent: Saturday, March 13, 2004 9:28 PM
> To: pym...@li...
> Subject: [PyMOL] Question about surface calculation
> 
> Hi All,
> 
> When I type "show surface", how is that surface calculated?  
> Is it a true solvent-accessible surface?  Does PyMol take 
> into account heteroatoms (e.g., a metal or an Fe-S cluster) 
> in the calculation?
> 
> -Fred
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials Free 
> Linux tutorial presented by Daniel Robbins, President and CEO 
> of GenToo technologies. Learn everything from fundamentals to 
> system 
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>