Re: [Jmol-users] MEP Surface Problem

2011-01-09 Thread Otis Rothenberger
Bob, If it helps, this is my message call back on MEP and VDW from the Jmol menu: isosurface1 created with cutoff=NaN min=0.0 max=0.0; number of isosurfaces = 0 The following point is not a problem, but I'll mention it because it might be related: isosurfaceArea The used to back as a decima

[Jmol-users] MEP Surface Problem

2011-01-09 Thread Otis Rothenberger
Bob, Molecular Electrostatic Potential appears to be broken on 12.1.30_dev. I can't map the surface via the Jmol menu or Jmol script on my page. The Jmol menu sees that partial charges are there, but no mapping occurs. Otis -- Otis Rothenberger Department of Chemistry Illinois State Univer

Re: [Jmol-users] fragmented 'cavity' isosurfaces

2011-01-09 Thread Robert Hanson
OK, thanks, Alexander. I see. Dots are not properly being filtered with isosurface SET or isosurface POCKET, and isosurface POCKET and SASURFACE got broken in this last installment of Jmol 12.1. Fixed for Jmol 12.1.30 and 12.0.27. Corrected 12.1.30 is at http://chemapps.stolaf.edu/jmol/docs/exampl

Re: [Jmol-users] fragmented 'cavity' isosurfaces

2011-01-09 Thread Robert Hanson
Oh, I see them now. Hmm... On Sun, Jan 9, 2011 at 7:04 PM, Robert Hanson wrote: > > > On Sun, Jan 9, 2011 at 5:49 PM, Alexander Rose < > alexander.r...@weirdbyte.de> wrote: > >> >> I drew them (http://dl.dropbox.com/u/3778149/1crn_surface-points.jmol) >> and notices that there are a lot of point

Re: [Jmol-users] fragmented 'cavity' isosurfaces

2011-01-09 Thread Robert Hanson
On Sun, Jan 9, 2011 at 5:49 PM, Alexander Rose wrote: > > I drew them (http://dl.dropbox.com/u/3778149/1crn_surface-points.jmol) and > notices that there are a lot of points in addition to the vertices of the > triangles that make up the surface. What are they? Can I get rid of them? > > They are

Re: [Jmol-users] fragmented 'cavity' isosurfaces

2011-01-09 Thread Alexander Rose
Hi, Am 21.12.2010 um 16:46 schrieb Robert Hanson: > The gridpoints are cleared from memory after use, and in many cases they are > "streamed" so as never to accumulate. But do you perhaps mean the vertices of > the triangles that make up the surface? You do have access to those points: > > pri