http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.16/
___JmolVersion="14.1.16"
JmolVersion="14.1.16_2014.05.29"
FEATURE CHANGE: jmolCommandInput 6th parameter added is default value
-- defaults to "help"
FEATURE CHANGE: set useArcBall removed
-- no longer necessary
-- arcBall is always used anyway
FEATURE CHANGE: removed UNITCELL "xxx" where xxx is an isosurface ID
-- undocumented
-- not necessary, as UNITCELL $xxx or UNITCELL isosurface xxx does as
well
FEATURE CHANGE: REMOVED: set fractionalRelative
-- an odd quantity -- related specifically to scripts commands
using {1/1 1/2 1/3} and cell=nnn
-- Its use with cell= was never documented.
-- It makes no sense to change the unit cell and not change the
meaning of {1/1 1/2 1/3} and cell=nnn
-- Only relates to situations where the unit cell has been offset.
-- Its presence caused unitcell [{origin} {a} {b} {c}] to fail.
-- It should never have been set in state, as it has nothing to do with
the state
FEATURE CHANGE: default space group names for Int. Tables # 39, 41, 64, 67,
68 added
new feature: moveTo AXIS [a,b,c,x,y,z]
-- rotates the model smoothly to a crystallographic or cartesian axis.
-- in the case of abc, the rotation places the remaining two axes
to the right and down (International Tables standard)
-- in the case of xyz, the rotation places the remaining two axes
to the right and up (standard Cartesian orientation)
-- for abc, if no unit cell is available, a simple {1 1 1 90 90 90} unit
cell is used
-- added to application and popup View menus
new feature: unitcell "type"
-- type can be "standard" or "parent" for now
derived from CIF records
-- "conventional" and "primitive" may follow
unitcell "standard"
unitcell "parent"
new feature: unitcell "abc_offset"
-- abc_offset is of the form "a,b,c;0,0,0"
where a, b, and c, can be any expression involving a, b, and c
and 0 can be an offset
-- numbers can be expressed fractionally or as decimals
-- offset is optional, but semicolon is not
-- effect is cumulative -- unit cell is NOT first restored
-- reversed using !
-- examples:
unitcell "a+b,a-b,c;1/4,1/4,1/4"
unitcell "!a+b,a-b,c;1/4,1/4,1/4"
unitcell "a+b,a-b,c;"
new feature: JSmol: allow for a user callback for customization of menu
if (Jmol._showMenuCallback)
Jmol._showMenuCallback(menu, x, y);
new feature: show(xxx) function
-- same as script("show " + xxx)
new feature: set showUnitCellDetails TRUE (default)
-- FALSE removes a,b,c,alpha,beta,gamma lines
new feature: unitcell RESET (or RESTORE)
-- returns unit cell to original values and removes offset and scaling
-- resets width to fine line
new feature: restore UNITCELL
-- returns unit cell to original values and removes offset and scaling
new feature: show symop n "fmatrix"
new feature: show symop @1 @2 "fmatrix"
-- gives rational fractional matrix
new feature: BilbaoReader NONORM option -- reads displacements as actual
values, not normalized
new feature: load ... filter "symop=..."
-- list of numbers separated by space, for example:
load quartz.cif packed filter "symop=2"
load quartz.cif packed filter "symop=2 3"
new feature: set echo depth x.x for standard echos
-- works for 3D echos now as well as 2D echos
-- values in percent of depth
-- x.x >= 1000 are (x.x % 1000) in front of the 3D position
-- x.x <= -1000 are (-x.x % 1000) behind the 3D position
new feature: set starWidth
-- replaces set set starScale
new feature: menu item color--atoms--by scheme--vectors
new feature: load "filename" packed x.x
-- x.x is the range in fractional coordinates within which an atom
can be close to being in the 555 cell but not quite and still be
accepted by the atom loading filter.
-- default is 0.02
-- in some cases, this adds too many atoms and can be reduced to 0.01 or
0.001
-- modulation reader uses 0.001 strictly.
-- for example:
load t2.bcs packed 0.01
{1.1}.property_dist = {1.1}.distance.min({1.2})
{1.1}.spacefill={1.1}.property_dist.all
color {1.1} property_dist "bwr" range 0 0.5
select 1.2
stars -0.3
set starwidth 0.1
frame *
unitcell {1.2}
new feature: Bilbao Crystallographic Server file reader
-- scrapes Bilbao HTML pages for Bilbao structure format
-- for example, http://www.cryst.ehu.es/cryst/compstru.html
or http://www.cryst.ehu.es/cryst/amplimodes.html
-- reads Bilbao standard setting data:
15
13.800 5.691 9.420 90.0 102.3 90.0
7
Pb 1 4e 0.0000 0.2910 0.2500
Pb 2 8f 0.3170 0.3090 0.3520
P 1 8f 0.5990 0.2410 0.4470
O 1 8f 0.6430 0.0300 0.3920
O 2 8f 0.6340 0.4640 0.3740
O 3 8f 0.6420 0.2800 0.6120
O 4 8f 0.4910 0.2220 0.4200
-- identified by 1st and third line being a single integer only
(IT spacegroup number and atom count, respectively)
new feature: unitcell {555 575 0}
-- 0 here means "draw these cells without internal lines"
-- (currently) .uxyz does not scale
new feature: dipole ID m1 ALL {...}
-- creates a molecular dipole set with ID
-- one dipole per molecule in specified range
-- connected to associated molecule in terms of visibility
new feature: unitcell OFFSET and RANGE
-- explicit parameters for unitcell {i j k} and unitcell {nnn mmm x}
new feature: unit cell display includes k (mCIF) and q (CIF, Jana2006)
vectors
bug fix: double-click drag doesn't drag the model, and
since double-click is determined by time, not location,
it appears as though sometimes the model drags and
sometimes it does not. Solution is to
a) add a localization to double clicking. I think that
was removed because of touch interface problems.
b) add left-double-drag to left-single-drag for standard rotation
bug fix: browser errant zero mouse move
causes collapse of rotation matrix
due to coding error in arcball routine
bug fix: drag-drop followed by model building may fail.
bug fix: tm.matrixRotate protected from setting to all zeros (Chrome issue;
reason unknown)
bug fix: JavaScript state creation not properly representing integral
decimal numbers
bug fix: draw length pt1 pt2 only makes half the line
bug fix: color $m* green blue wild card coloring for isosurfaces doe not
work
bug fix: {*}.trace = {*}.bfactor crashes Jmol (.bfactor does not exist)
bug fix: ramachandran plot scaling off
bug fix: color $isosurface1 "rwb" range 3.0 4.5 fails to set color scheme
bug fix: write VAR X fails if X is an associative array
bug fix: show NMR broken
bug fix: H1 simulation not happening in Jmol.jar
bug fix: write() function does not work for write("coords")
bug fix: vibration vectors may have incorrect length if vector scale and
vibration scale are different
bug fix: LOAD ... SUPERCELL not saved in state
bug fix: CASTEP reader not handling supercell correctly (packing and
phonons)
bug fix: Jmol 14.1.12 broke atom.fxyz for models that have vibrations.
-- atom.fxyz SHOULD change with changes in unit cell, but when an update
was
made to accommodate modulated subsystems, where different atoms in a
model may have different unit cells, this capability was lost for any
atom having any sort of vibration other than a modulation.
bug fix: set hoverlabel will be ignored if no hover has already taken place
bug fix: symmetry operation drawing/description with centering
bug fix: Bilbao uses 2nd origin for numerous spacegroups
bug fix: magCIF reader using 4x4 determinant, not 3x3
bug fix: file drag-drop doing append if no atoms
bug fix: BilbaoReader amplimode correction
bug fix: polyhedra not vibrating
bug fix: application file open preview not working
bug fix: show file only shows file for model 1.1
bug fix: signed applet not accepting drag-drop
bug fix: getProperty "fileInfo" for CIF should fix keys (lower case and
change '.' to '_')
bug fix: problems reading PNGJ files for Jana2006
code: faster calculations involving point-based atom properties such as fx
code: TransformManager clean-up;
code: Viewer/FileManager clean-up; image loading moved to jzu
--
Robert M. Hanson
Larson-Anderson 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
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