[Jmol-users] Jmol 11.3.40

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

Nico has released Jmol 11.3.40. This release adds several new features 
and fixes some bugs.

NEW FEATURES
------------

MATH: SET Command no longer for user variables
----------------------------------------------
Using

  set x 3

will now cause an error. The proper way to assign user variables is

  x = 3

The idea here is to make a clearer distinction between user variables 
and Jmol parameters. You can still do

  antialiasDisplay = true

you just can't do

  set antilaiasDisplay true

[because it's mis-spelled]

Recommendation is to use SET for all Jmol parameter setting, and "=" for 
user variables. For your own sanity only.


MATH: model-based parallel array calculations
---------------------------------------------
The .split() function now separates a set of atoms into a list by model.

   x = {atomno < 10}.split()  # a list, one element for each model
   select @{x[3]} # the atoms 1-9 in the third model

Operations such as .add(), .sub(), .mul(), .div(), .x, .y, .xyz, etc. 
all work on the list elements individually, thus doing parallel 
per-model calculations.
 
The draw command recognizes these lists to be "per model" specifications:

   draw myPts @{{atomno = 3}.split().xyz.sub({1 0 0})}

draws a set of points, one per model, offset from the third atom by 1 
unit in x.


MATH: point3f in array()
------------------------
You can now mix and match variable types in an array:

  xlist = array({1,2,3}, {1,1,0}, "red", 3, 3.5, "Testing")
  print xlist[1]+{1 0 0};
  color atoms @{xlist[3]}


DRAW: title lines are titles for each model
-------------------------------------------
Previously only the first title line was used in draw titles. Now each 
line of a multi-model draw object corresponds to each model.


RAMACHANDRAN: Better Plots
--------------------------

 ramachandran

command now creates one plot per model. You can have as many 
Ramachandran plots as you have models.

 model

command by itself switches back to the model corresponding to the 
Ramachandran plot currently being viewed.


NEW READER: MoldenReader (Matthew Zwier <mc...@gm...>)
------------------------------------------------------------


MOLECULAR ORBITALS (Matthew Zwier <mc...@gm...>)
------------------------------------------------------

Adds MO calculations for spherical orbital basis sets (6D orbitals, F 
orbitals)


BUG FIXES
---------

# bug fix: select within(1.0,{x y z})

# bug fix: draw object text not selective for frame

# bug fix: noninteger MO occupancies

-- 
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