Jmol 14.32.17

Bug fix: Show $s2 for isosurface reports first isosurface only
Bug fix: _M.unitCellParams does not update after modifying the unit cell
Bug fix: GausssianReader Tensor "csa" broken
Bug fix: ScriptEditor many issues
Bug fix: ... HKL {1 1 1} works, but HKL 1 1 1 fails, if not last in a command
New feature: getproperty("atomInfo").select("fx,fy,fz"):
Adds fractional coordinates to atomInfo
New feature: draw boundbox @1 @2 @3 @4:
Draws a boundbox with edges in the x, y, and z directions through a set of points
New feature: draw best boundbox @1 @2 @3 @4:
Draws the best boundbox through a set of points
New feature: draw best plane @1 @2 @3 @4:
Draws the best plane through a set of points
New feature: draw best line @1 @2 @3 @4:
Draws the best line through a set of points
New feature: draw intersection [unitcell or boundbox description] [line or plane description]:
Intersects all types of boundboxes and unitcells with any type of plane or line
New feature: draw intersection [unitcell or boundbox description] ON [line or plane description]:
Projects a unitcell or boundbox on any plane
New feature: draw intersection [unitcell or boundbox description] LINE @1 @2:
Extends the specified line to intersect a unitcell or boundbox
New feature: draw diameter -1:
For lines or mesh option
Draws a simple line with 1-pixel width
New feature: draw diameter -n:
For lines or mesh option
Draws a dotted 1-pixel line with alternating n on, n off pixels
New feature: draw HKL {1 1 1 x.x}:
Offsets an HKL plane from the origin by x.x Angstroms
New feature: draw HKL {1 1 1} OFFSET x.x:
Alternative to HCL {1 1 1 x.x}

bug fix: isosurface intersect unitcell broken
bug fix: show spacegroup does not report H-M name

bug fix: reading of protein structure for a group that is not in a polymer causes null pointer exception

bug fix: set platformSpeed 1 for pmesh fails bug fix: polyhedron EDGES fails
bug fix: @{ {"hash":{0.1 0.1 0.1},...} } fails (attempts to turn "," into "OR") solution is to not allow "," for OR within associative arrays

bug fix: if (...) \n { .... not working bug fix: CIF reader will read empty second model for IUCr files with terminal data_global block
bug fix: polyhedra bonds unitcell can cause error in HTML5
bug fix: nucleic backbone should include O atoms on P and C bug fix: nucleic spine should not include C2'
bug fix: pmesh/isosurface RESOLUTION 0.0001 with plane can cause loss of some or all of the plane -- resolution 0.0001 creates just a minimum of triangles to construct the plane.
bug fix: set testflag4;isosurface ... ; does not generate normals
bug fix: (Application) set refreshing false shows Jmol console in model frame (Java bug??)

bug fix: load files "xxx.png|xxxx" "xxx.png|zzzz" not read from state properly
bug fix: polyhedra not saved in state property
bug fix: moving atoms with 4x4 matrix not saved in state
bug fix: moving of an atom having a polyhedron fails to move the polyhedron as well
new feature: smiles2.find("SMILES",smiles1, asMap, allMappings)

feature change: DSSR reference to "lonePairs" changed to "isolatedPairs"
select within(dssr,"isolatedPairs") preferred
select within(dssr,"lonePairs") still OK
bug fix: msCIF reader incorrectly handling multiple Legendre orders
bug fix: msCIF reader incorrectly handling superspace operators with x1,x2,x3 mixed into x4,x5
bug fix: CONTACT FULL does not report proper volume (Young ho Jhon)
bug fix: (Java only) write FILE fails for string (copy/pasted) data

feature change: IDTF exporter now calling media9 rather than movie15 in accompanying TeX file
new feature: JSmol Info.z, Info.zIndexBase
new feature - set cartoonRibose:
draws in ribose rings, with facets showing puckering
connects via C4'-C5'-O5'-P explicitly
shows C3'-O3' for reference.
disables cartoonBaseEdges (Leontis-Westhof Edges)
disabled by SET cartoonBaseEdges ON
suggested by Rick Spinney, Ohio State
new feature: anim frame [a,b,c,d] works with negative numbers to indicate ranges:
anim frame [1, -5, 10, -6] --> [1,2,3,4,5,10,9,8,7,6]
read as "1 through 5 and then 10 through 6"
new feature - Tinker file reader (and FoldingXYZ reader upgrade):
Can use Tinker:: but this is only required if first line is JUST an atomCount
accommodates older Tinker format with n-1 atoms for atomCount
allows for trajectories and desired model number
new feature: (actually 13.1 but undocumented) animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....]
new feature: x = compare({atomset1}, {atomset2}, "MAP") new feature: x = compare({atomset1}, {atomset2}, "MAP", "all")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "best")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "H")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "allH")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "bestH")
generates one or more correlations lists based on non-aromatic SMILES
optionally includes H atoms -- optionally generates all possible atom mappings
returns int[][] = [ [a1 b1],[a2 b2],[a3 b3],... ] where an and bn are integer atom indices or list when "all" option is chosen.
the following will generate one atom correlation map for two structures including hydrogen atoms:
load files "a.mol" "b.mol"
x = compare({1.1} {2.1} "MAP" "H")
(useful for 2D/3D model atom matching)
the following compares the model of caffeine from NCI to that from PubChem:
load $caffeine;load append :caffeine;frame *
select 2.1; label %[atomIndex]
compare {1.1} {2.1} SMILES rotate translate
x = compare({1.1}, {2.1}, "MAP" "bestH")
for (a in x) {a1 = a[1];a2=a[2];select atomindex=a1;label @a2}
new feature: compare {model1} {model2} SMILES
no need to give SMILES; Jmol can generate it from {model1}
new feature: x = {*}.find("SMILES", "H")
generates SMILES with explicit H atoms
bug fix: set defaultLoadScript "{0 0 0}" actually sets that to {1 1 1} - goes way way back to early Jmol math where there were no point-type variables
bug fix: PyMOL reader update for Version 1700 lacking setting 83.
bug fix: -m option not working with Jmol.jar
bug fix: PNGJ files within ZIP collections not being read.
full PNGJ models can be extracted from MS Word .docx files.
bug fix: tensor("efg", "value") should return sparce array, not dense for missing tensors
bug fix: JSmol now allows writing POVRAY, MAYA, IDTF, VRML, etc. both from Java and from HTML5
code: reworking of export classes
bug fix: label @{math expression...} not working
bug fix: interpretation of x and @x in select commands and {...} phrases Variable substitution has been unintuitive and inconsistent.
bug fix: for(i in ...) does not exit when i is assigned a value, as per documentation
bug fix: for(x in ...) command broken and also quite inefficient.
bug fix: substructure() function using SMILES instead of SMARTS, so only full structures;
bug fix: better error trapping and messages in SMILES-related methods
bug fix: make webexport discovery of path to Jmol.jar and jsmol.zip more robust.
bug fix: getProperty extractModel not honoring subset
bug fix: set pdbGetHeader TRUE does not capture REMARK3 REMARK290 REMARK350
bug fix: getProperty("JSON",....) should wrap value in {value:...}
bug fix: MO persistent translucency broken in 11.x
bug fix: show MENU write MENU load MENU all broken in 12.2
bug fix: {*}[n] should be empty if nAtoms 80%
code: JSmol: applying atom mapping between mol2D and mol3D for viewSets
code: refactoring to enable SWING in javascript for all menus
code: methods from jcampdxReader extracted to org.jmol.jsv.JDXMOLParser
code: reader overhaul for setting atom coordinates in a consistent fashion

new feature - set cartoonRibose:
draws in ribose rings, with facets showing puckering
connects via C4'-C5'-O5'-P explicitly
shows C3'-O3' for reference.
disables cartoonBaseEdges (Leontis-Westhof Edges)
disabled by SET cartoonBaseEdges ON
suggested by Rick Spinney, Ohio State
new feature: anim frame [a,b,c,d] works with negative numbers to indicate ranges:
anim frame [1, -5, 10, -6] --> [1,2,3,4,5,10,9,8,7,6]
read as "1 through 5 and then 10 through 6"
new feature: Tinker file reader (and FoldingXYZ reader upgrade):
Can use Tinker:: but this is only required if first line is JUST an atomCount
accommodates older Tinker format with n-1 atoms for atomCount
allows for trajectories and desired model number
new feature: (actually 13.1 but undocumented) animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....]
new feature: x = compare({atomset1}, {atomset2}, "MAP")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "all")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "best")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "H")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "allH")
new feature - x = compare({atomset1}, {atomset2}, "MAP", "bestH"):
generates one or more correlations lists based on non-aromatic SMILES
optionally includes H atoms
optionally generates all possible atom mappings
returns int[][] = [ [a1 b1],[a2 b2],[a3 b3],... ]
where an and bn are integer atom indices or list when "all" option is chosen.
the following will generate one atom correlation map for two structures including hydrogen atoms: load files "a.mol" "b.mol" x = compare({1.1} {2.1} "MAP" "H")
the following compares the model of caffeine from NCI to that from PubChem:
load $caffeine;load append :caffeine;frame *
select 2.1; label %[atomIndex]
compare {1.1} {2.1} SMILES rotate translate
x = compare({1.1}, {2.1}, "MAP" "bestH")
for (a in x) {a1 = a[1];a2=a[2];select atomindex=a1;label @a2}
new feature: compare {model1} {model2} SMILES:
no need to give SMILES; Jmol can generate it from {model1}
new feature: x = {*}.find("SMILES", "H"):
generates SMILES with explicit H atoms
bug fix: substructure() function using SMILES instead of SMARTS, so only full structures;
bug fix: better error trapping and messages in SMILES-related methods
bug fix: make webexport discovery of path to Jmol.jar and jsmol.zip more robust.
bug fix: getProperty extractModel not honoring subset
bug fix: set pdbGetHeader TRUE does not capture REMARK3 REMARK290 REMARK350
bug fix: getProperty("JSON",....) should wrap value in {value:...}
bug fix: MO persistent translucency broken in 11.x
bug fix: show MENU write MENU load MENU all broken in 12.2
bug fix: {*}[n] should be empty if nAtoms

bug fix: unitcell and echo rendering, getProperty

new feature: Jmol._j2sLoadMonitorOpacity (default 55)
new feature: load() function, as in print load("xxx"), limited local file reading in applet:
no root-directory files
no files without extension
no files with any "/." in path
new feature: JAR files securely signed
new feature: applet JAR files include JNLPs (Java Network Launch Protocols) for local file loading
new feature: JSmol URL options _USE= _JAR= _J2S= overrides for Info data
new feature: (was present but undocumented) print quaternion([array of quaternions]) - returns spherical mean a la Buss and Fillmore
new feature: print quaternion([array of quaternions], true):
returns standard deviation for spherical mean a la Buss and Fillmore
units are angular degrees
new feature - named quaternion modulus values:
print quaternion(1,0,0,0)%"matrix"
options include w x y z normal eulerzxz eulerzyz vector theta axisx axisy axisz axisangle matrix
ew feature - set celShadingPower:
sets strength of cel shading
integer values
default 10 is a thick line
5 is a fine line
0 turns cel shading off
negative value removes interior shading -- outline only
operates on pixel based on normal to light source (power > 0) or user (power < 0)
sets color to background contrast (black or white) when normal_z < 1 - 2^-(|celShadingPower|/10)
new feature: mmCIF reading reports _citation.title in Jmol scripting console
new feature: minimize SELECT {atomset} ONLY - ONLY option excludes all other atoms
new feature: minimize {atomset} - implicit SELECT and ONLY
new feature -"extensions" directories in JSmol for contributed JS and SPT scripts:
jsmol/js/ext
jsmol/spt/ext
new feature: load ... filter "ADDHYDROGENS" - local set pdbAddHydrogens just for one load command
new feature: compare {1.1} {2.1} BONDS SMILES
new feature: list = compare({atomset1} {atomset2} "SMILES" "BONDS")
new feature: write JSON xxx.json
new feature: [#210] JSON {"mol":...} reader
ew feature - set particleRadius :
global radius for atoms over the max radius value (16.0)
defaults to 20.0
new feature - CIF and PDB filters "BYCHAIN" and "BYSYMOP" for virus particulation:
creates just one atom per chain or per symop
size can be scaled larger than the max of 16 Angstroms using, for example:
set particleRadius 30;
spacefill 30; // any number over 16 here uses particleRadius instead
new feature: list = compare({atomset1} {atomset2} SmartsString "BONDS")
new feature: symop() function allows symmetry from biomolecule filter for PDB and mmCIF
new feature - isosurface SYMMETRY:
applies symmetry operators to isosurface
more efficient rendering and creation
default selection is {symop=1} only
default coloring is to color by symop based on propertyColorScheme
example:
load 1stp filter "biomolecule 1"
color property symop
isosurface sa resolution 0.8 symmetry sasurface 0
new feature - new atom property: chainNo:
sequentially from 1 for each model;
chainNo == 0 means "no chain" or chain = ''
new feature - new propertyColorScheme "friendly":
color-blindness-friendly color scheme
used at RCSD
new feature: JSpecView completely Java-free; includes 2D nmr and PDF printing of spectra
new feature - WRITE PDF "xxx.pdf" quality > 1 requests landscape mode:
uses efficient custom PDF creation classes
sizes image to fit if too large
new feature: JSpecView adds PDF and 2D NMR for javascript
new feature: load "==xxx" FILTER "NOIDEAL" - Chemical component load from PDB using the "nonideal" coordinate set
bug fix: write CD removed; ChemDoodle has changed formats; use JSON instead
bug fix: PDB and CIF files indicated assemblies such as PAU as large negative number
bug fix: COMPARE with no rotation starts infinite loop
bug fix: looping problem with delay(-1)
bug fix: Mouse wheeling for Chrome in javascript
bug fix: javascript popup menu fix for language changes
bug fix: javascript core components not being processed; Jmol._debugCode not recognized
bug fix: unitcell offset incorrectly for biomolecules; origin incorrect for axes.
bug fix: isosurface/mo FRONTONLY broken
bug fix: language localization broken in javascript
bug fix: ADF reader not reading MO output from DIRAC Build 201304052106
bug fix: Safari reports yellow Jmol info instead of asking to accept applet
-- tag needed to be
bug fix: CIF reader not handling _pdbx_struct_assembly_gen.assembly_id properly
-- wrong atom set for load =3fsx.cif filter "ASSEMBLY 1"
bug fix: [#558 Compatibility issue with ChemDoodle] JSmol error in definition of Number.toString()
bug fix: mouse wheel not working properly
bug fix: javascript J2S compiler error does not coerce int += float to integer
bug fix: javascript WEBGL option broken
bug fix: javascript NMRCalculation does not access resources
bug fix: javascript stereo not implemented
bug fix: MOL reader fix for multiple-model file (just 13.3.9_dev)
bug fix: MOL reader error with load APPEND -- does not continue atom numbers
bug fix: CIF modulation reader not reading linear combinations of cell wave vectors
bug fix: CIF reading with filter "BIOMOLECULE 1" fails if only the identity operation
bug fix: mmCIF reader not reading all _pdbx_struct_assembly_gen.oper_expression options
bug fix: PDB CRYST entry 1.0 1.0 1.0 90 90 90 should mean "no unit cell" regardless of biomolecule filter
bug fix: isosurface slab not adapting well for flat molecules such as HEM
bug fix: print userfunc() may fail (userfunc() by itself is fine)
bug fix: within(helix) not implemented for C-alpha-only polymers
bug fix: _modelTitle not updated when a new file is loaded or zapped
bug fix: {*}.symop.all not delivering symmetry operator appropriately
bug fix: for triple bond in SMILES in URLs
bug fix: build.xml missing PDF creation classes
bug fix: following Java update, adding proper path check for local signed applet
bug fix: {xxx}.property_xx not saved in state (broken 8/7/2013 rev 18518)
bug fix: Manifests updated for signed and unsigned applet JAR files
bug fix: write fails
bug fix: applet scriptWait() method broken
bug fix: PyMOL session may display unit cell after read from saved state
bug fix: MMCIF reader fails for multiple assembly types
bug fix: CIF reader "biomolecule 1" translating to "molecular" rather than "assembly"
bug fix: load trajectory with multiple files not working
bug fix: JS applet popup menu not closing properly upon language change
bug fix: HTML checkbox id attribute not assigned
code: refactoring of applet/appletjs code; org.jmol.util.GenericApplet
code: refactoring, simplification of buffered readers and buffered input streams.
code: javascript refactoring, better build_...xml
code: javascript Integer, Long, Short, Byte, Float, Double all reworked
code: disambiguation of GT._
code: Refactored all unnecessarily inner classes to top level
code: isolated util/ModulationSet using api/JmolModulationSet
code - All applet language localization read from plain .po files :
as for javascript already
no need to compile class files for applet languages
no language .jar files
new jsmol/idioma directory holds .po files for both Java and HTML5
code: faster isosurface rendering adding implicit "frontonly" with select {xxx} ONLY
code: faster isosurface rendering with implicit "isosurfacepropertySmoothing FALSE" in relevant (integer) cases
code: JmolBinary.getBufferedReaderForResource() - consolidates all references to URL.getContent() and Class.getResource()
code: javascript work around for inner class problem with variable name reassignment
code: work-around for eval(functionName) not working in javascript.
code: experimenting with ambient occlusion
code: Required manifests added for Java Ju51 (January, 2014).
code: JmolOutputChannel moved to javajs.util.OutputChannel
code: jsmol.php fixed to allow " in saveFile method
code: refactoring Parser into javajs.util
code: DSSP moved to org.jmol.dssx, reducing JSmol bio load by 20K
code: iText package jettisoned, no longer nec, as I wrote my own PDF creator