[Jmol-users] integral of isosurface

2012-06-23 Thread Daniel Aioanei
For a small molecule I can compute an electrostatic potential-mapped isosurface like this: isosurface name sasurface 1.4 map color range min max '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

[Jmol-users] show isosurface for water molecule sasurface freezes GUI

2012-06-23 Thread Daniel Aioanei
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

Re: [Jmol-users] Applet Fatigue

2012-06-23 Thread Otis Rothenberger
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

Re: [Jmol-users] Applet Fatigue

2012-06-23 Thread Angel Herráez
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 longer

Re: [Jmol-users] show isosurface for water molecule sasurface freezes GUI

2012-06-23 Thread Eric Martz
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

Re: [Jmol-users] integral of isosurface

2012-06-23 Thread Robert Hanson
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

Re: [Jmol-users] Applet Fatigue

2012-06-23 Thread Robert Hanson
but the signed applet works fine -- just not the unsigned applet. On Sat, Jun 23, 2012 at 11:25 AM, Angel Herráez angel.herr...@uah.eswrote: 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