http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.06.14b.zip
testing appreciated -- I would like to release a new version of Jmol 14.2
before the end of the week.
Jmol.___JmolVersion="14.3.15_2015.06.13"
bug fix: var firstPARAM = "p1_b"; x = [FIRSTParam: "p1_a"]; results in
lowering of case as [firstparam:....]
bug fix: set drawPicking draw;set drawpicking does not show handles
bug fix; point group not calculated when the selected atoms are a subset of
a model
bug fix: x.find("SMILES") is incorrect for structures that have hypervalent
atoms and branches such as inorganic nitrates
bug fix: msCIF reading with two models, and only one has displacement
modulation causes "render error" crash
bug fix: msCIF reader failing for Legendre polynomials of order greater
than 4
bug fix: DRAW for quadrilateral broken when perspective depth is turned off.
bug fix: SET ECHO IMAGE broken in JavaScript version
feature note: This version introduces several very powerful and very
different capabilities
to Jmol in the area of crystallograpy. Many of these features
are nonexistent
in other programs. They involve:
- 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 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}]
- 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")}
new feature: POLYHEDRA 12 UNITCELL
-- creates a polyhedron (12-gon in this case) around each of the
currerntly selected atoms that has that bonding environment
-- DOES NOT require atoms at these positions - can simply use the
unit cell and periodicity to find the relevant atom positions.
-- will check bonding as necessary using autobonding parameters
-- accepts all standard polyhedra options. For example:
polyhedra 12,16 3.5 UNITCELL
new feature: POLYHEDRA 4-16
-- allows a range of unit cell bonding patterns.
-- in this case, same as 4,5,6,7,8,9,10,11,12,13,14,15,16
polyhedra 4-16 3.5 UNITCELL
new feature: getProperty shapeInfo.polyhedra
print getProperty("shapeInfo.polyhedra[1]").keys
_ipt
center
modelIndex
planeCount
polygons
vertexCount
vertices
new feature: draw POINTS [ array of points ]
draw diameter 0.2 points
@{getProperty("shapeInfo.polyhedra[1].vertices")}
new feature: show pointgroup POLYHEDRON
-- uses points from the polyhedron of the first selected atom
-- recommended to use specific atom reference in POLYHEDRA command:
select @21
polyhedron 3.5 UNITCELL
show pointgroup polyhedron
$ show pointgroup polyhedron
# 13 atoms
Oh Ci {2.1020985 -4.3122215 2.1430104}
Oh nC4 3 2
Oh C4_1 {0.99993926, -0.007795072, 0.0077921236}
Oh C4_2 {7.8514034E-7, -0.9997856, -0.020707628}
Oh C4_3 {7.619045E-7, 0.009661385, -0.9999533}
Oh nC3 4 2
Oh C3_1 {-0.58944535, 0.5712053, 0.57120806}
Oh C3_2 {-0.58944565, -0.5712049, -0.57120824}
Oh C3_3 {-0.5824926, -0.58349025, 0.5658989}
Oh C3_4 {0.5764604, -0.5864354, 0.5690228}
Oh nC2 9 1
Oh C2_1 {0.7004682, -0.71362424, -0.0092081865}
Oh C2_2 {0.7004673, 0.009209763, 0.7136251}
Oh C2_3 {0.99993926, -0.007795072, 0.0077921236}
Oh C2_4 {-0.70046806, -0.71362436, -0.009208187}
Oh C2_5 {-8.22445E-7, 0.7071046, -0.707109}
Oh C2_6 {7.8514034E-7, -0.9997856, -0.020707628}
Oh C2_7 {0.7056006, -0.019795598, -0.70833325}
Oh C2_8 {7.619045E-7, 0.009661385, -0.9999533}
Oh C2_9 {5.440252E-7, 0.70734024, 0.7068733}
Oh nS6 4 2
Oh S6_1 {-0.58944535, 0.5712053, 0.57120806}
Oh S6_2 {-0.58944565, -0.5712049, -0.57120824}
Oh S6_3 {-0.5824926, -0.58349025, 0.5658989}
Oh S6_4 {0.5764604, -0.5864354, 0.5690228}
Oh nS4 2 2
Oh S4_1 {0.99993926, -0.007795072, 0.0077921236}
Oh S4_2 {7.619045E-7, 0.009661385, -0.9999533}
Oh nCs 9 1
Oh Cs_1 {0.0, 0.7071068, -0.7071067}
Oh Cs_2 {0.0, -0.7071068, -0.7071068}
Oh Cs_3 {0.007949507, 0.020366998, -0.999761}
Oh Cs_4 {0.007952394, 0.999761, -0.020367}
Oh Cs_5 {1.0, 0.0, 0.0}
Oh Cs_6 {0.7030396, 0.014484465, 0.71100324}
Oh Cs_7 {0.7030395, 0.71100324, 0.014484464}
Oh Cs_8 {0.70023495, -0.008727634, -0.7138592}
Oh Cs_9 {0.7030395, -0.71100324, -0.014484464}
Oh type nType nUnique
Oh E 1 1
Oh Ci 1 1
Oh Cs 9 9
Oh Cn 16 23
Oh Sn 6 12
Oh TOTAL 46
-- displays a table showing point group information.
-- notice that not all the operators may be found because of settings of
set pointGroupDistanceFactor 0.2 being too tight a restriction.
new feature: draw POINTS <list of points or array of points>
new feature: draw POLYGON <list of points or array of points> -1
-- these two are identical; POINTS is a bit nicer.
load "file:/C:/temp/aflow/binary/AgCd.aflow_binary" 20 //filter
"ca=0.5;nopack"
select @1 & 1.1
polyhedra 4-16 3.7 unitcell
x = within(4, true, "unitcell", {selected})
print x;
draw width 0.2 points @{x["points"]} color red mesh nofill translucent
new feature: select POLYHEDRA
-- selects central atoms of any atoms having polyhedra.
new feature: select polyhedra(4)
-- selects central atoms of any atoms having tetrahedral polyhedra.
new feature: x.find("SMILES","*")
-- creates a topology SMILES, involving just * and connections
-- does not include stereochemistry
-- allows comparison of connection patterns without respect to any other
consideration.
-- can be used to check equivalences in inorganic crystal structures.
code: SMILES code cleaned up.
code: most image loading is now asynchronous. (Not BMP, not from PNGJ files
with "|" in filename)
code: introducing interfaces to allow less use of @j2sNative and more
traceability of method calls in Eclipse
bug fix: polyhedra broken for number of vertices > 6.
-- needed smaller default distanceFactor (set to 1.5; formerly 1.85)
-- this setting is for any
--
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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