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[Jmol-users] Jmol 14.1.16 released
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From: Robert H. <ha...@st...> - 2014-05-29 14:35:16
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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 |