This update takes care of a few minor bugs and also introduces several
powerful features in relation to polyhedra, unit cells, and SMILES.
Jmol.___JmolVersion="14.4.4_2016.03.21"
released
new feature: moveto axis [a1-c4]
-- extends moveto axis a|b|c to all for corners 1|2|3|4
where 1 is upper left, 2 is upper right, 3 is lower right, and 4 is
lower left
-- for example, MOVETO AXIS a3
-- defaults: a==a1, b==b1, c==c4
new feature: axes OFFSET x.x
-- applies offset of x.x in fractional coordinates in each axis direction
-- AXES OFFSET -0.1 same as AXES CENTER {-0.1 -0.1 -0.1/1}
new feature: expanded unitcell() function
-- adds additional types: "A", "B", "C", "I", "F"
-- default is the lattice type of the model's space group
-- not just cubic; "BCC" is converted to "I"
-- for example:
load =ams/silicon 15 packed // Cmca
draw id "uc" diameter 0.1 unitcell mesh nofill color black
unitcell @{unitcell("primitive")}
color unitcell red
unitcell 0.1
axes unitcell
axes on
new feature: expanded UNITCELL command to include PRIMITIVE option for any
space group
new feature: show smiles/NCI aka show smiles/CACTVS aka show
smiles/canonical
-- generates nonaromatic SMILES and sends that to NCI for canonicalization
bug fix: SMILES matcher not allowing azulene to be aromatic
bug fix: OpenSMILES matcher not allowing non-chemist Hueckel 4+2
interpretation
bug fix: SMILES generator not adding "-" for biphenyl Ar-Ar bond
bug fix: set picking invertSTEREO does not work on open-ring systems
bug fix: SMARTS [R] matching all atoms
bug fix: dashed lines not visible in measurements, unit cells, and axes
bug fix: axes 0.01 produces thick 20-pixel-wide lines
-- solution was to drop that to 0.001 for this effect
bug fix: Polyhedra with verticies that are also centers of polyhedra for
atoms that were visible
but are no longer visible do not update screen positions properly
--
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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