[Jmol-users] Time for another Jmol version: 11.1.28

[Bob H. <ha...@st...>]

Jmol 11.1.28 is ready for inspection at 
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm

and will be downloadable from SoureForge soon.

Something for everyone in here. Most importantly, 11.1.28 does change 
three default properties.

CHANGED DEFAULT RENDERING FOR MOLECULAR ORBITALS TO: MESH NOFILL FRONTONLY

11.1.28 introduces MUCH improved MESH rendering for surfaces such as 
molecular orbitals. This is now the default rendering for the MO 
command. If this is not what you wish, you can go back to the old 
"opaque" standard using

  MO FILL NOMESH

before or after the command you use to produce the MO.


CHANGED BEHAVIOR FOR ISOSURFACE COMMAND WITHOUT ID INDICATED:
  
Previously, if you created an isosurface but did not indicate a name for 
it, then a new isosurface with a numerically assigned name was created. 
"isosurface1", "isosurface2", etc.
Unfortunately, this makes it way too easy to create a whole bunch of 
isosurfaces that you don't want and you can't tell are there because 
they overlay each other. So I considered that a "bug" and fixed it. Now 
if no ID is indicated, the previous ID is used for all commands that 
create a new isosurface, thus replacing that isosurface with the new 
one. This means, for example, that you can check out different 
parameters without worrying about deleting or naming:

isosurface sasurface 0
isosurface sasurface 1.0
isosurface molecular

just produces one isosurface, then changes it to different types.

CHANGED BEHAVIOR FOR ISOSURFACE DEFAULT COLOR
  
The default isosurface color no longer changes shade among 5 possible 
shades.
That was necessary only because it was easy to mistakenly make multiple
isosurfaces that otherwise would look the same.


New file support -- MOPAC graphf output (.mgf files)
----------------------------------------------------
Jmol now reads coordinates, charges, and molecular orbitals from 
openMOPAC calculations. This work was done in coordination with Jimmy 
Stewart, developer of MOPAC. A new version of MOPAC2007 
http://openmopac.net/ is being released simultaneously with Jmol 11.1.28 
to support this new file type.


New file support -- Fujitsu Sygress (formerly CAChe) reading (.csf files)
-------------------------------------------------------------------------
Jmol 11.1.28 adds support for CAChe CSF files with MOPAC (AM1, PM3, etc.),
Density Functional, Gaussian, and Extended Huckel molecular orbitals.
  

New MO Command Options
----------------------
 
    mo HOMO [+/- n]
    mo LUMO [+/- n]
   

allow for easy display of HOMO and LUMO orbitals or orbitals near them.


New Isosurface-Related Command Options
--------------------------------------
 
Jmol 11.1.28 makes it easier to see what the IDs of isosurfaces are with 
the LIST option:

  draw list
  isosurface list
  lcaocartoon list
  (mo list) -- not particularly useful
  pmesh list
 
Listing gives id, number of vertices, number of polygons, visibility,
and title (usually the command that was given that created this isosurface)
  


New SCRIPT function
-------------------
Jmol 11.1.28 adds
  
  a = script("some script command")
 
putting output into a from commands such as "show" or "getProperty", for 
instance. For example:

  a = script("show symmetry")
  a = a.lines.find("Spacegroup")
  message @a

New JAVASCRIPT function
-----------------------
Jmol 11.1.28 adds
  
  a = javascript("some javascript")
  
for getting user input, for example, DURING a script:

  a = javascript("prompt('Enter a label for carbon atoms')")
  select carbon
  label @a


New JAVASCRIPT command
-----------------------------
Now you can execute JavaScript directly in Jmol:

  javascript alert("OK")


for example.


Note that JavaScript evaluation with either of these methods can be 
disallowed (as, perhaps, for Wikis) using

 _jmol.noEval = true

within the calling page.

Bob Hanson