Nico has released 11.3.33, which has several interesting new features
and a few bug fixes:
#version=11.3.33
# _PovrayExporter adds draw, halos, stars, dipoles, vectors, polyhedra,
# backbone, cartoons, meshRibbon, ribbon, rockets, strands, trace,
# dots, geosurface, molecular orbitals, LCAO cartoons, pmesh,
# single-color isosurfaces
Get ready for serious graphics. This is actually quite exciting, and I
hope people will give it a try. To produce a POV-Ray image from the Jmol
application, now just use the script:
write povray "myfile.pov"
Jmol will also write a POV-Ray initialization file, myfile.pov.ini, that
specifies input and output file names and image type, among other
things. Of course, you can use your own ini file, but this one is set to
write a PNG file.
To actually DO the rendering you will need POV-Ray. I used the Windows
edition and found it very easy to use. The only problem is that when I
get the image I keep trying to rotate it with the mouse!
-- Thanks to Pim for getting this going
The rendering of atoms and bonds is spectacular. The implementation is a
bit incomplete:
-- only crude triangulation of unmapped isosurfaces
-- no mapped isosurfaces
-- no atom labels, axis labels, 2D, or 3D echos
We'll keep working on this as the feedback comes in.
# new feature: site_ support for PDB and CIF
#
# loading of PDB and CIF files containing site information
# automatically defines variables site_xxx and defines selections
site_xxx and site_n
# where xxx is the site identifier and n is the site number.
# These settings are reset each time a file is loaded.
# They do not carry over from one file to the next.
Try this with
load =1hf4
and then
select site_1
select site_ac1
select site_ac2
script inline "select " + site_list.join(","); spacefill on;
-- Thanks to Eran for bringing this to my attention. Maybe we can get
a menu setting....
# Web Export Dialog changes: new intro tab, new minilog at bottom,
instructions converted to
# buttons which open the info in the standard Jmol Help Dialog.
-- Thank you, Jonathan Gutow.
# adds support for " xx' " atom designations in PDB and variable names
You can now use single quotes where needed in PDB atom specification and
also in variable names:
a = 3
a' = 4
print a + a'
> 7
-- Thanks to Angel and Rolf for researching this.
# new feature: inline scripting allows math
#
# script INLINE "select " + site_list[2]
This means you can construct a select command from variable pieces and
execute it directly.
bug fixes include:
# bug fix: rockets color incorrect for head groups
# bug fix: "OP1" and "OP2" as backbone designators (new PDB designation)
# bug fix: insertion codes stored incorrectly in 11.3.32
# bug fix: [xxx] in select commands, where xxx can be ANY valid PDB
residue designation.
Bob
--
Robert M. Hanson
Professor of Chemistry
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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