Daniel,
On Sun, Jun 24, 2012 at 2:19 PM, Daniel Aioanei <[email protected]> wrote:
> A few more questions on the same topic:
>
> 1. Are "isosurface vdw 1.4" and "set solventProbe 1.4; isosurface
> molecular" exactly the same thing?
>
>
No, not at all. vdw 1.4 is the same as sasurface 1.4 (a solvent-accessible
surface, not
a solvent-excluded surface; without excluding solvent)
"isosurface solvent 1.2" is the same as "isosurface molecular" (default) and
"isosurface solvent 1.4" is the same as "solventProbe=1.4;isosurface
molecular"
> 2. What I need is the locus of points at a distance of vdw(X) + 1.4
> Angstroms of at least one atom X and at least as large as vdw(Y) + 1.4
> Angstroms for any atom Y. I think that's the usual definition of the
> "surface accessible area", but I may be wrong. Are the two commands
> suggested, namely "isosurface vdw 1.4" and "set solventProbe 1.4;
> isosurface molecular", compatible with the above description?
>
>
[solvent-accessible] Just change "molecular" there to "sasurface" and you
have it.
> 3. I have a pqr file which contains the radius of each atom in the
> molecule. Is it possible to replace vdw(atom) + 1.4 with radius(atom)
> + 1.4, where each atom can have a different radius? Note that atoms at
> different positions in the molecule can have different radii, even if
> they have the same atomic number.
>
>
Reading the PQR file does already store the "R" field as vdw radius. That's
automatic.
Be careful with hydrogens. I think Jmol assigns 1.0 instead of pqr's 0 to
some of those. In the PQR reader we have
if (atom.radius < 0.9f)
atom.radius = 1;
There's a note there:
// based on parameters in
http://pdb2pqr.svn.sourceforge.net/viewvc/pdb2pqr/trunk/pdb2pqr/dat/
// AMBER forcefield, H atoms may be given 0 (on O) or 0.6 (on N) for
radius
// PARSE forcefield, lots of H atoms may be given 0 radius
// CHARMM forcefield, HN atoms may be given 0.2245 radius
// PEOEPB forcefield, no atoms given 0 radius
// SWANSON forcefield, HW (on water) will be given 0 radius, and H on
oxygen given 0.9170
What's your idea there? How do you want to work around that? I could write
a filter that allows you to load the actual (sometimes 0) vdw radii for
hydrogens, if you need that. And, come to think of it, I should probably
just have the PQR reader also store the actual values in that field into
the temperature or occupation property anyway so that you can retrieve that
if you ever want to.
Bob
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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