All changes in Jmol 14.3.15 have now been merged into Jmol 14.2.15.
synchronized with 14.3.15_2015.07.09
The list of new features is probably too long for this message. You can see
the whole list here:
https://sourceforge.net/p/jmol/code/HEAD/tree/branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Some highlights:
feature note: This version introduces several very powerful and very
different capabilities
to Jmol in the area of crystallography.
The polyhedra command has been extended significantly,
allowing for much
more interesting polyhedra and also the extraction of
polyhedron information.
Polyhedra can now be SEARCHED using SMILES and SMARTS as
though they were
molecules.
Many of these features are nonexistent in other programs.
They involve:
- new MACRO command allows us to build macros that can be used generally
- the ability to adjust the lattice scaling using filter
"latticeScaling=0.98"
thus allowing comparison of structures with slightly different lattices
- the ability to load a given block of space (such as a 10x10x10-Angstrom
cube)
with a crystal structure irrespective of its given unit cell.
(Are these two structures that have totally different unit cells really
that different?)
load t.cif FILL
load t.cif FILL 20
load t.cif FILL {20 10 10}
load t.cif FILL [{0 0 0} {5.2 5.2 0} {-5.2 5.5 0} {1.3 0 3.3}]
- an extension of SMILES to compare bonding topology irrespective of atom
identity.
(Are these two atom environments both iscoahedral?)
x = {@1 and 1.1 and connected(@1)}.find("SMILES", "*"}
y = {2.1}.find("SMARTS", x)
- the generation of polyhedra in crystal structures for which only the
central atom
may be loaded.
(What is the atom environment around Au3 in this crystal structure?)
load t.cif // just the unit cell, maybe just one atom even
polyhedra 4-12 UNITECELL @1
- the ability to show and draw the point group of a polyhedron
load t.cif
polyhedron 12 unitcell @1
select @1
show pointgroup POLYHEDRON
draw pointgroup POLYHEDRON
- the ability to extract information about polyhedra
print getProperty("shapeInfo.polyhedra[1]").keys
_ipt
center
modelIndex
planeCount
polygons
vertexCount
vertices
- the ability to select polyhedra
select polyhedra
select polyhedra(4)
print polyhedra()
print polyhedra(4)
- the ability to draw points from derived arrays
draw diameter 0.2 points
@{getProperty("shapeInfo.polyhedra[1].vertices")}
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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