Re: [Jmol-users] surfaces and JVXL files

Sat, 19 Aug 2006 17:33:07 -0700

Thanks to Hens, Bob, and everyone who replied to me on this question. I'm happy to hear I can create the surface in Jmol and I will be testing out the instructions soon.

What a great users list.

Frieda 


On Aug 18, 2006, at 3:07 PM, Hens Borkent wrote:

Hi Frieda,

While Bob is crossing the ocean: As I understood it, JVXL files can be 
generated from any surface displayed by Jmol.
The JVXL lines are written to the Java console (if your browser has 
one......Mine at home hasn't, so I can't test what I'm writing here).
The source of the surface could be a CUBE file, but not necessarily.
Cube files (often very large) are produced by quantum chemistry programs 
(Gaussian in particular) to describe orbitals or electron density, and 
the surface (at a particular contour level) can be written out in the 
much smaller JVXL format. This doesn't apply to macromolecules.
For proteins something like "surface resolution 6 solvent 3.0" should 
create a solvent-excluded surface, after a while. Or "surface sasurface 
radius" for the solvent accessible one. Also this surface could be 
written out by the applet in JVXL format, and it might be more efficient 
to offer the JVXL file on your web page rather then recalculating it by 
the surface command.

Hens

Hi All,

I am interested in fast rendering of surfaces for large molecules. It 
seems that Bob Hanson has invented a file format for this purpose, 
called JVXL. I have seem Angel Herraez's and Bob's test pages for 
surfaces, but I am still puzzled as to how to get started in doing this.

To create a JVXL surface file in Jmol, do you first have to load a 
CUBE file into Jmol? I have started to read a little about CUBE files 
but am unfamiliar with them. How do you generate a CUBE file?

Frieda

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Frieda Reichsman, PhD

Molecules in Motion

Interactive Molecular Structures

http://www.moleculesinmotion.com


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