Jmol.___JmolVersion="14.2.11_2015.01.20"
released simultaneously with 14.3.11
see
http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.11/
FEATURE CHANGE: JmolViewer interface streamlined
-- many esoteric methods removed
-- can be reinstated upon request
-- many are available via public fields
-- for economy of performance and .js file size
FEATURE CHANGE: "screened translucency TRANSLUCENT -1" removed (broken in
jmol-11.7.27_02-27-09)
FEATURE CHANGE: For the ISOSURFACE command, there is an undocumented
syntax that the CUTOFF keyword prior to a number is optional,
as in "ISOSURFACE 2.0". This was never documented and was never
shown in any examples. This change is to require the CUTOFF keyword
new feature: Jmol Application Tools|NBO... (Experimental Only; requires
NBOServer)
new feature: modulation T x.x
new feature: modulation Q n
new feature: modulation T {t1 t2 t3}
new feature: modulation Q {q1 q2 q3}
new feature: CGO (undocumented command from Jmol 13.1.16; never tested)
cgo test1a [
BEGIN LINES
VERTEX 0 0 0 VERTEX 2 2 2
VERTEX 2 2 2 VERTEX 3 2 0
END
]
cgo test1b [
BEGIN LINE_LOOP
VERTEX 4 0 0 VERTEX 6 2 2
VERTEX 6 2 2 VERTEX 5 2 0
END
]
cgo test1c [
BEGIN LINE_STRIP
VERTEX 4 0 0
VERTEX 6 2 2
VERTEX 5 2 0
END
]
cgo test2 [
BEGIN POINTS
COLOR 255 0 0
LINE 0 0 3 0 0 3 2 2
COLOR 0 255 0
LINE 0 0 3 2 2 4 2 0
END
]
cgo test2b [
BEGIN LINE_LOOP
DIAMETER 0.3
VERTEX 4 0 0 VERTEX 6 2 2
VERTEX 6 2 2 VERTEX 5 2 0
END
]
new feature: NBO command
-- same as MO command, but allows TYPE keyword
-- to be developed with, perhaps, different defaults, 2D slices, etc.
new feature: NBO TYPE <nboType>
-- options AO, PNAO, NAO, PNHO, NHO, PNBO, NBO, PNLMO, NLMO, MO
-- results in immediate loading of .32-.41 file if present
-- generally after a .47 archive file has been loaded
new feature: ... PLANE {pt1} {pt2} frac12
-- wherever a PLANE parameter is required
-- perpendicular plane frac12 of the distance from pt1 to pt2
new feature: x = plane(pt1, pt2, frac12)
-- perpendicular plane frac12 of the distance from pt1 to pt2
new feature: SYNC nnnn x
-- x is a math expression, possibly just a string, but also possibly an
associative array.
new feature: SYNC nnnn {type:"command", "command" : command, "var": vname,
"data":vdata}
-- script command request, with optional definition of a Jmol user
variable prior to execution)
-- for example:
x = {"type":"command","command":"background green; print y", "var":
"y", "data":['an array',2]}
sync 3000 x
-- allows simple transfer of data via JSON strings between applications
new feature: reset LIGHTING
public void resetLighting() {
vwr.setIntProperty("ambientPercent", 45);
vwr.setIntProperty("celShadingPower", 10);
vwr.setIntProperty("diffusePercent", 84);
vwr.setIntProperty("phongExponent", 64);
vwr.setIntProperty("specularExponent", 6); // log2 of phongExponent
vwr.setIntProperty("specularPercent", 22);
vwr.setIntProperty("specularPower", 40);
vwr.setIntProperty("zDepth", 0);
vwr.setIntProperty("zShadePower", 3);
vwr.setIntProperty("zSlab", 50);
vwr.setBooleanProperty("specular", true);
vwr.setBooleanProperty("celShading", false);
vwr.setBooleanProperty("zshade", false);
}
new feature: Castep reading of .ts files
new feature: MODEL 1 PROPERTY "xxx" x
-- adds property to model's auxilliaryInfo
-- x may be any valid math expression, for example
model 1 property "test" {1.1}.temperature.mul(0.1)
-- if x is an array, then these become atom data accessible via %{...}
-- for example:
x = "1\n2\n3\n".lines
model 1 property "mydata" x
{model=1}.property_n = {*}.label("%{mydata}") // converts to numbers
data "myd @x" // similar, but not model-based
label %{myd}
new feature: "....".split("",true) // CSV split of string to array of arrays
new feature: [...].split("",true) // CSV split of array to array of arrays
new feature: "...".split("\t",true) // tab split of string to array of
arrays
new feature: [...].split("\t",true) // tab split of array to array of arrays
new feature: [...][...].join("",true) // CSV join to array of lines
new feature: [...][...].join("\t",true) // tab join to array of lines
-- example:
x = load("test.csv").split("",true) //from CSV
print x.join("",true) // back to CSV
print x.join("\t",true) // to tab-separated
new feature: [...][...].col(n)
-- extracts nth column from an array of arrays
-- example:
x = load("test.csv").split("",true).col(3) //3rd column from CSV
new feature: Gaussian Input File creation defaults to "opt pop=full
gfprint" to generate orbital information by default.
FEATURE CHANGE: Gaussian Input File creation moved to Tools menu rather
than file...export
new feature: readers for ESS input types: CFILE, VFILE, MOPAC, NWChem,
Gaussian, GAMESS, Orca, PQS
-- CFILE and VFILE require CFI:: and VFI:: (or C:: and V::)
-- MOPAC requires MND::
-- any of these could also use ZMATRIX:: or INPUT::
new feature: GAMESS input reader
new feature: NBO .37 archive file coordinate reader (not MOs)
new feature: ZMatrixReader also serves as simple input file reader
for Q-Chem, Gaussian, Jaguar, MolPro, and ADF, as produced by
NBO6Pro
new feature: isosurface contour 0 "t.jvxl" will override contour selected
in JVXL file
new feature: isosurface CONTOUR n i
-- n contours; i-th only
new feature: isosurface LATTICE {i j k} FIXED
-- creates an isosurface from periodic volumetric data
with the specified number of unit cells
-- "fixed" in the sense that the operation is at load time
not at rendering, allowing slabbing and use of WITHIN
new feature: isosurface UNITCELL x.x ....
-- for periodic lattices only
-- adjusts grid by x.x in fractional coordinates
-- caution is advised, as the grid is expanded in this process,
leading to more grid points and more memory required
-- negative x.x results in a selection of a subset of the data
centered on the center of the unit cell
new feature: VASP CHGCAR default cutoff set to 0.5
new feature: set edsUrlFormatDiff
-- specifies difference map location
new feature: isosurface "==1blu"
-- difference map fo-fc
-- defaults to sigma=3
-- automatically implements SIGN option
new feature: isosurface RMSD (same as SIGMA)
bug fix: Languages lost in Jmol Application
new feature: select :"X" where quotes are used now forces case sensitivity
bug fix: DIPOLE command broken in Jmol 14.3.10_2014.11.27 (OK in 14.2)
bug fix: for old PDB files with no chain ID, "select :" fails
bug fix: Typing select his and :A will set chain selection to be case
sensitive due to a bug that
processes "his an" as "{his:}an".
bug fix: modulation x.x and modulation n not described correctly in
documentation
bug fix: color PMESH reader not working properly
bug fix: JSpecView -- version/date not appearing in menu
bug fix: GIF images bleed into background.
bug fix: GIF writing of xxx.gif (three character name) broken.
bug fix: proper isosurface caching. Test code:
function test(i) {
set echo top left
echo @i
isosurface slab none
isosurface cap plane {1 1 1 1} @i
refresh
}
load 1crn.pdb
rotate y 60
rotate y -120
isosurface s1 vdw;
display none
center $s1
for (var i = -2 ; i < 58; i++){test(i)}
bug fix: JavaScript connect broken
due to j2s failure to create bsAromatic when BondCollection
created (14.3.7)
due to j2s bug in instantiating global definitions in super
classes using Clazz_prepareFields
bug fix: label, echo, and measurement text should not display when deeper
than zSlab with zShade is TRUE
bug fix: mmCIF reader load filter biomolecule 1
broken for viruses with symmetry ranges listed as "1-60" with a
hyphen
bug fix: mmCIF reader coarse-grain load filter bysymop broken
bug fix: mmCIF reader coarse-grain load filter bychain broken
bug fix: rotate selected <4x4 matrix> should not rotate about center of
atoms
bug fix: use of a subset command will change value of a variable bitset if
"select x" is used
-- example:
x = {*}
subset {atomno < 10}
print x // just the first 9
select x // just the first 9
subset all
print x // but now x itself is truncated; this is not supposed to be the
case
bug fix: mol2 reader fails to read "THR1" as a PDB group
bug fix: PyMOL reader should not reset user variables
bug fix: show LIGHTING does not report a full list of settings
bug fix: array.add("\t",array) broken 2014.12.04
bug fix: array.split("",true) doesn't handle CSV with new lines in quotes
bug fix: format() function broken
bug fix: SHOW DATA should be cleared when a file is loaded
bug fix: for (x in yUpperCase) fails
bug fix: draw SYMOP fails for incommensurate space groups
bug fix: incommensurate magnetic CIF reading does not apply magnetic spin
operation to spin modulations
bug fix: CIF reader can cycle infinitely if loop_ keywords are not followed
by any data
bug fix: dynamicMeasurements deprecated in 14.1.1 but
not left in as a valid token to allow use
bug fix: SPIN BRANCH {atomno=2} {atomno=1} does not work
bug fix: JVXL files do not record selected contour
bug fix: isosurface CONTOUR -n broken (in Jmol 12)
bug fix: isosurface "t.jvxl" loading of contoured planes broken
bug fix: isosurface plane xy map property atomno broken every other time
used
bug fix: hover OFF disables hover callback, but should not
bug fix: reading of JVXL file saved with noFill still does fill
bug fix: CASTEP DENSITY surface file reader does not do downsampling
code: major refactoring into BioModel of PDB-specific code in ModelSet
code: moved PDB-related methods and constants in JC.java to
org.jmol.modelsetbio.Resolver
-- allows 50K savings in core.z.js
code: reduced method sets for Viewer, ModelSet, and several other classes
-- a bit contrary to standard practice, I know
-- direct access of class fields instead of using methods with just one or
two references
-- direct access of class fields instead of using getXXX() and setXXX()
because these are NOT optimized in JavaScript.
code: scriptExt.IsoExt splits CmdExt into two parts
code: simplification of SurfaceGenerator
--
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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