Two issues there.
1) SASURFACE and SOLVENT automatically exclude water. For small molecules
or to not exclude water, use:
isosurface vdw 1.4
or
set solventProbe 1.4; isosurface molecular
2) That's a bug when the number of vertices is 0. That's fixed, but for now
just don't do that.
Bob
On S
but the signed applet works fine -- just not the unsigned applet.
On Sat, Jun 23, 2012 at 11:25 AM, Angel Herráez wrote:
> On 23 Jun 2012 at 11:31, Otis Rothenberger wrote:
> > This might be useful, but I'm frustrated that I blew getting the
> JmolScript history. Formerly, this
> > text could sim
Daniel,
I would suppose you would need the set of vertex positions, vertex values,
and faces. Then you would need some sort of algorithm that would give you
the integration across a triangle that has three different values, one on
each vertex. Summing over all the faces would give you the integral
Not sure if its helpful, but this page shows a translucent isosurface
for water colored by molecular electrostatic potential, in Jmol 12.3.22. -Eric
http://proteopedia.org/wiki/index.php/User:Eric_Martz/Sandbox_8
At 6/23/12, Daniel Aioanei wrote:
>I'm not able to compute the sasurface of a water
On 23 Jun 2012 at 11:31, Otis Rothenberger wrote:
> This might be useful, but I'm frustrated that I blew getting the JmolScript
> history. Formerly, this
> text could simply be copied. Did something change in Java security related to
> this?
Yes, after some Java version update, text can no lon
Bob,
This might be useful, but I'm frustrated that I blew getting the JmolScript
history. Formerly, this text could simply be copied. Did something change in
Java security related to this?
Anyway, here's the point of possible interest: While trying to cause this
error, I kept my eye on the Jav
I'm not able to compute the sasurface of a water (H2O) molecule:
$ isosurface test sasurface 1.4
test created with cutoff=0.0; isosurface count: 0
$ show isosurface
$
After the above commands, I cannot see any surface drawn, and in fact
after issuing the "show isosurface" command, it's not possib
For a small molecule I can compute an electrostatic potential-mapped
isosurface like this:
isosurface sasurface 1.4 map color range
'pymol-generated.dx' translucent .2
zoom 40
Once I have the surface, how can I compute the integral of an
arbitrary function of the electrostatic potential on the
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