___date=$Date: 2012-10-02 23:25:07 +0200 (mar., 02 oct. 2012) $
___fullJmolProperties=is src/org/jmol/viewer/Jmol.properties
# NOTE: This is not the development trunk, this is the release branch.
# No new features should be added, just bug fixes for 13.0.
# Developers: to add a description of changes you have made,
# add it on a line below the "___version=..." line.
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
___version=13.0.6
bug fix: PDB 4B2Q, with faulty (incomplete) REMARK 350 not read
version=13.0.5
bug fix: CASTEP PHONON files not loading
=============================================================================
version=13.0.4
bug fix: translate selected x ... bug
bug fix: ISOSURFACE saving in state broken 7/30/12 in 13.0.RC3
bug fix: simple isosurface PLANE not saved in state
bug fix: isosurface command with MAP from state when saved to state may fail
=============================================================================
version=13.0.3
bug fix: CUBE reader reading atom Z numbers as partial charge
=============================================================================
version=13.0.2
bug fix: translate x 0 does not recenter the model in the window
bug fix: PDB polymers of length 1 allow size to be set and appear {visible} but are not
bug fix: OPEN dialog doesn't allow for no PDB cartoons.
bug fix: open dialog for 1-residue PDB files does not show atoms.
bug fix: pngj storage of Spartan directory zip files or Spartan directories cannot be read
because the PNGJ files created do not contain the necessary files from the directory
=============================================================================
version=13.0.1
APPLET:
-- a new OOP JavaScript interface (Jmol-JSO)
allowing nonJava options such as ChemDoodle and GLmol
as well as JME/JSpecView connectivity
-- JmolData full "headless" operation for server-side processing
BIOPHYSICS:
-- COMPARE command
FILE READING:
-- reading of JCAMP-DX files having structure/spectra assignment data
using ##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview)
-- Gaussian log reading of Natural Transition Orbitals
-- automatic PNGJ file caching for immensely faster loading of PNGJ files from remote servers
FILE WRITING:
-- write PNGJ files encapsulate all model file data into one PNG file
-- write image 400 400 PNGJ "http://....." POSTs JMOL or IMAGE or structure to a server as application/octet-stream
-- write MOL adds partial charge data as > <JMOL_PARTIAL_CHARGES> in SDF format
-- multiple-scene PNGJ files allowing minimal or full data loading and scripted animations
ISOSURFACES:
-- isosurface caching
-- isosurface MOVE [[...matrix4f...]] moves/rotates an isosurface (for the state)
MINIMIZATION:
-- MMFF94/UFF minimization and energy calculation
MOLECULAR DATA:
-- show CHEMICAL
-- show NMR
MOLECULAR PLAYGROUND:
-- MolecularPlayground -- remote status and remote control
SOLID-STATE PHYSICS:
-- solid state physics support
SPECTROSCOPY:
-- integration of JSpecView into Jmol, including 2D spectral display and manipulation
STRUCTURE SEARCHING:
-- extended Jmol SMARTS searching
-- PubChem search for name (which can be a CAS number), cid, or SMILES using ":"
=============================================================================
version=13.0.RC7_dev
bug fix: isosurface CAVITY not saved in state
=============================================================================
version=13.0.RC6
bug fix: isosurface CAVITY not saved in state
bug fix: Gaussian reader not reading "AO basis set in the form of general basis input" properly ("Gen" keyword)
bug fix: Gaussian reader not reading "7D 0" correctly
bug fix: Trajectories still broken for PDB files
code: all import foo.*; removed, specified
=============================================================================
version=13.0.RC5
bug fix: broke trajectories in 13.0.RC4
=============================================================================
version=13.0.RC4
new feature: write SCENE PNG|PNGJ "xxxx.spt" option to create PNG or PNGJ files (same file, just different extension)
new feature: "menu" as sole contents of a script pops up the context menu
-- joins category of special commands, including "exit" "pause" and "quit"
bug fix: load append TRAJECTORY (upper case) fails
bug fix: load append trajectory "$mannose" fails (loads two models)
bug fix: load trajectory "maleic.cif" fails with cryptic error message (not appropriate for trajectory loading)
bug fix: undocumented and inaccurate CALCULATE VOLUME removed
=============================================================================
version=13.0.RC3
new feature: automatic PNGJ file caching for immensely faster loading
new feature: write MOL adds partial charge data as > <JMOL_PARTIAL_CHARGES> in SDF format
new feature: isosurface CACHE <surface creation parameters> ....
-- parameter CACHE along with isosurface creation or alone instructs Jmol to
immediately create JVXL data for the specified surface and to load that data instead.
The surface remains in memory (in this version of Jmol) can can be used again
using cache://isosurface_<ID> where <ID> is the isosurface ID such as "isosurface1".
-- The command ISOSURFACE CACHE alone will cache the current isosurface
-- If the cache is no longer needed, then RESET CACHE will release the memory used to hold the JVXL data for the isosurface
-- The result should be essentially equivalent to the original command.
(It is recommended that the original be a relatively simple command, because not all nuances
of an isosurface may be stored in the JVXL data.)
-- THIS OPTION IS NOT COMPATIBLE WITH SAVING THE STATE AS AN SPT FILE.
-- Instead, one needs to save the state in PNGJ or JMOL format, where the cached isosurface
can be reloaded from a file saved in the PNGJ or JMOL zip directory
bug fix: load a model, then load append TRAJECTORY -- will fail
bug fix: load APPEND xxx where xxx is FILE, INLINE, SMILES, TRAJECTORY, MODEL
all save incorrect LOAD command in state
bug fix: shelx reader (.res) not assigning space group name or applying normalization
=============================================================================
version=13.0.RC2
bug fix: isosurface molecular producing artifacts
bug fix: isosurface select {...} molecular not excluding all other atoms for troughs
new feature: Gaussian log reading of Natural Transition Orbitals
new feature: isosurface MOVE [[...matrix4f...]] moves/rotates an isosurface (for the state)
bug fix: isosurface moved by atom connection not saved correctly in state
bug fix: isosurface SET n not read properly from JVXL file.
ant fix: changing the way Jmol.properties is handled vis-a-vis # and underscores
bug fix: isosurface SOLVENT producing artifacts --- needed minimum resolution
bug fix: isosurface with selected set not delivering just those vertices for within distance calc
bug fix: isosurface CONNECT in documentation but never implemented
bug fix: isosurface SET n not saved in state or JVXL file.
bug fix: Gaussian reader fails for 2-digit basis orbital names such as "12XX"
bug fix: PNGJ creation not handling same-file or same-name issues.
bug fix: isosurface SOLVENT producing cavity-like artifacts
bug fix: SCENE writing with toggle (pause scene 2 ... pause scene 2) in error
bug fix: SCENE min spt script needs wrapping by pathForAllFiles
bug fix: isosurface MINSET or SET not compatible with SLAB
bug fix: show $d1 where d1 is a DRAW object broken
bug fix: calculate hydrogens incorrect for proteins
=============================================================================
version=13.0.RC1
-- a new OOP JavaScript interface allowing nonJava options and JME/JSpecView connectivity
-- MMFF94/UFF minimization and energy calculation
-- integration of JSpecView into Jmol, including 2D spectral display and manipulation
-- reading of JCAMP-DX files having structure/spectra assignment data
##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview)
-- multiple-scene PNGJ files allowing minimal or full data loading and scripted animations
-- write PNGJ files encapsulate all model file data into one PNG file
-- extended Jmol SMARTS searching
-- show CHEMICAL
-- show NMR
-- solid state physics support
-- MolecularPlayground -- remote status and remote control
-- COMPARE command
-- JmolData full "headless" operation for server-side processing
-- PubChem search for name (which can be a CAS number), cid, or SMILES using ":"
-- isosurface caching
-- write image 400 400 PNGJ "http://....." POSTs JMOL or IMAGE or structure to a server as application/octet-stream
=============================================================================
version=12.3.33 (13.0.RC1)
new feature: full JSpecView support for NMR
-- integration, peak listing, measurements
-- printing with peak measurements
new feature: measure(a b "minArray")
-- measures minimum distance from atom set a to atom set b atom by atom
-- return array with number of elements corresponding to the number of selected atoms
-- for example: {1.1}.property_distTo12 = measure({1.1}, {1.2} "minArray"); color property_distTo12
new feature: {x}.property_d = [....]
-- allows for [....] to have length of the number of atoms in {x}
in which case the values are assigned on a 1:1 basis
new feature: PDB reader reads gromacs-created "pdb_wide_format" files
and also automatically reads PQR based on gromacs REMARK
bug fix: select within(1.0, withinallmodels, 1.1) and 1.2 causes exception
bug fix: script xxx(yyy).spt broken
=============================================================================
version=12.3.32
FEATURE CHANGE: LOAD "myfile.xxx" with no additional parameters
where xxx is "png" or "pngj" or "spt"
now assumes these are scripts and runs SCRIPT "myfile.spt" instead
new feature: write SCENE "xxxx.spt"
-- creates pngj files
-- using "xxxx.png" will STILL USE "xxxx.spt" but will create PNGJ files with ".png" extensions
-- scene creation with linked PNGJ files
-- xxxx.spt should include "pause scene n" commands, which are then
used to separate the script into separate scenes. "n" must be an integer.
-- Two files are created for each scene (pngj unles:
xxxx_scene_n.min.pngj very small; does not contain anything more than
an image, JmolManifest.spt, and scene.spt
xxxx_scene_n.all.pngj adds all necessary files, plus script.spt
-- Either of these files can be used, but if x.min.pngj is used,
then x.all.pngj needs to be present as well in the same directory.
new feature: drawHover displays ID for isosurface and reports to hoverCallback
new feature: load "$$xxxxx" loads 2D version, not 3D (used for JmolData connection with JME)
-- basically, use of two $ signs results in drop of "&get3d=True" from NCI call
bug fix: compiler not synchronized; allows jmolEvaluate() to fail if two threads access it simultaneously
bug fix: getproperty isosurface after a "no-surface" isosurface call like load $water;isosurface sasurface fails
bug fix: color for hbonds/ssbonds backbone incorrect
=============================================================================
version=12.3.31
bug fix: isosurface plane ... within ... map ... fails
bug fix: write broken in 12.3.30
=============================================================================
version=12.3.30
new feature: atom properties sx, sy, sz, and sxyz -- screen coordinates
new feature: app flag -r restricts file access
-- like -R, but allows reading of ".spt" files
new feature: load("http://.....?POST?_PNGJBIN_")
-- accompanies load("http://....?POST?_PNG_") and load("http://....?POST?_PNGJ_")
-- sends PNGJ image to server as byte array instead of as application/octet-stream
instead of Base64-encoded string and application/x-www-form-urlencoded
-- return value is whatever server is set up to send
new feature: select within(distance, $drawID)
bug fix: isosurface plane... map property temperature not working
bug fix: PNG files written by Jmol from 12.3.7 - 12.3.29 have incorrect
checksum. Browsers do not seem to care, but Java does
when loading a background image in Jmol!
bug fix: background image NONE fails
bug fix: if(...) statement (no braces) broken in 12.3.21
=============================================================================
version=12.3.29
new feature: (JmolCore.js/JmolApplet.js/JmolCD.js/JmolApi.js)
-- changes "useChemDoodleOnly" to "disableJmol"
in preparation for non-ChemDoodle plug-ins similar to JmolCD.js
-- allows for default values for Info
-- adds Info.src
-- similar to src in an <image src="xxx.png" /> tag
-- turned into LOAD "xxx.png"
-- more efficient coding
new feature: set MESHSCALE (default 1) also allows isosurface/mo mesh scaling
-- was DOTSCALE in 12.3.26, but that is not appropriate
new feature: Mopac archive reader, including internal coord. defs
-- use FILTER "NOCENTER" to NOT center atoms in unit cell
-- use CENTROID for complete molecules with centroids within unit cell
-- use PACKED CENTROID for complete molecules with any atoms within unit cell
-- properties stored in auxiliaryInfo
use getProperty auxiliaryInfo or x = getProperty("auxiliaryInfo".foo) to retrieve
new feature: set pathForAllFiles "..."
-- all files, local or remote, will be taken from the indicated path
-- the indicated path may be a zip file entry (ending with "|")
-- automatically reset to '' in case of an unrecoverable error in execution
-- used for creating JMOL files containing user scripts instead of a state
-- disallows all writing and image creation
-- scripts including prompts to read wildcard files (for example, "load ?")
will still prompt for those and read them properly
new feature: write SCRIPT ["scriptFileName", "filename2","filename3",...] PNGJ|JMOL...
-- syntax is WRITE SCRIPT followed by an array of file names
then whatever else is necessary to create the PNGJ or JMOL file
-- for example: write script ["wind.spt"] test.jmol
-- Creates a single PNGJ or JMOL file that instead of containing the state
contains the script and additional files listed by the user.
The first script is run, and it is presumed that the other files are
needed for full execution of that script.
-- Allows for creating PNGJ and JMOL files that run as animations, not just final states.
-- Jmol will automatically add any files current to the state,
but other files not indicated by the state (script files especially)
required for the script to run need to be indicated by the user.
-- When the script is executed, pathForAllFiles is set to the zip file
itself. Thus, even scripts containing references such as "script2.spt" or "=xxxx"
can be run, provided the user supplies script2.spt xxxx.pdb.gz as one of the required filenames.
-- Note that if a file is saved locally using LOAD =xxxx AS t.pdb, Jmol will automatically use
the local file reference to t.pdb, not the RCSB reference.
-- If the file is loaded using only LOAD =xxxx, then Jmol will reload the
remote file and store it in the PNGJ/JMOL file as xxxx.pdb.gz.
bug fix: Jmol 12.3.28 breaks writing JMOL/PNGJ files
-- Jmol 12.3.28 release DELETED
bug fix: modelkit mode creating atoms after load "@x" fails
bug fix: script javascript:xxxx() broken for Jmol object javascript
bug fix: JmolCore.js fix for getPropertyAsArray
bug fix: draw arrows not adjustable using set picking draw
bug fix: Exception for select within(molecule,...) when atoms have been deleted
=============================================================================
version=12.3.28
DELETED 6/10/2012 due to breaking of JMOL/PNGJ format
new feature: isosurface ... map PERIODIC ...
-- allows mapping grid-based data beyond the unit cell defining its grid
new feature: write VIBRATION n
-- writes 20 * n frames
-- n periods
-- some issues with first frame and value of n
new feature: load PACKED CENTROID
-- only complete molecules having one or more atoms within or on the face of the unit cell
-- may not preserve # of atoms of unit cell
-- reverts to simple PACKED if this is a single-molecule solid (such as diamond)
new feature: unitcell $isosurfaceID
new feature: unitcell [{center}, {a}, {b}, {c}]
-- sets unit cell for current model only
new feature: "plot data" command by itself opens a new frame with just one atom in it, at (0,0,0)
new feature: isosurface SLAB BRILLOUIN (or WIGNERSEITZ)
-- transposes an isosurface into the Brillouin-zone/Wigner-Seitz unit cell
-- based on the isosurface's vectors if there is no unit cell for this model.
-- for creating isosurfaces of Fermi surfaces
bug fix: LOAD with SPACEGROUP or RANGE or UNITCELL should default to {555 555 -1} (packed) lattice
bug fix: JVXL reading of mapped data does not use file's rendering option for lighting
bug fix: default measure dotted lines are too thin for export
bug fix: measures not offset correctly when given width in line.
=============================================================================
version=12.3.27
new feature: [menu] vibration [*,/] 2
new feature: XSF isosurface reader
new feature: load CENTROID
-- only complete molecules having centroid in unit cell
-- preserves # of atoms of unit cell
bug fix: write PNGJ broken in 12.3.26
bug fix: 12.3.26 breaks Jmol/JspecView connection
bug fix: draw pointgroup scale x.x -- changing x.x does not revise point group
bug fix: reading of JVXL-version 1 (nonXML) files does not display colors
bug fix: translate y 10 works, but translate Y 10 does not
=============================================================================
version=12.3.26
new feature: Jmol SMARTS searching can include full Jmol selection syntax within
an atom primitive using the "atomType" option and "select:":
load caffeine.xyz
print {*}.find('{c}$(select _N and connected(2, _C))')
new feature: model ID "xxx" (or frame ID....)
-- sets the model's ID to "xxx"
-- can be used to switch to that model using model "xxx"
-- can be targeted file-specifically using "filename#xxx"
-- if two models have the same ID and no filename is given,
then the first model found becomes the current model
-- used for correlating non-Jmol synced applets
new feature: script "t.spt"(...variables...)
-- quotes are optional if file name does not include " " or "("
-- "script" is optional if file name is quoted or ends with ".spt"
-- allows passing variables to a script much like a function call
-- variables will be in VAR named "_arguments" within that script (like JavaScript)
-- _arguments, like all arrays in Jmol, is 1-based, 0-terminated (unlike JavaScript)
-- _arguments is unsettable by the user
-- for standard script functions, _arguments will be []
-- for example, if test.spt is simply "show _arguments", then
load $caffeine
test.spt({*}, {*}.xyz ,35, [1,2,3,4])
will output:
_arguments = [({0:23}),{-0.086670786 -0.02787502 5.6667876E-4},35,[1,2,3,4]]
new feature: set forcefield "UFF" or "MMFF"
-- default is MMFF
-- automatically switches to UFF if atom types cannot be set
-- minimizationCallback reports actual force field used
new feature: set energyUnits kJ|kcal
new feature: antialiased display and image creation uses larger mesh scaling for cleaner look
code: adding empirical rules to MMFF94 calculation
checkmm.spt;checkAllEnergies
checking calculated energies for 761 models
1 COMKAQ E= -7.3250003 Eref= -7.6177 diff= 0.2926998
2 DUVHUX10 E= 64.759995 Eref= 64.082855 diff= 0.6771393
3 FORJIF E= 35.978 Eref= 35.833878 diff= 0.14412308
4 JADLIJ E= 25.104 Eref= 24.7038 diff= 0.4001999
5 PHOSLA10 E= 111.232994 Eref= 112.07078 diff= 0.8377838
6 PHOSLB10 E= -93.479004 Eref= -92.64081 diff= 0.8381958
for 761 atoms, 6 have energy differences outside the range -0.1 to 0.1
with a standard deviation of 0.05309403
bug fix: nested SMARTS strings can give incorrect response
load data "mol"
C:/jmol-dev/bobtest/t6.mol
__Jmol-12_05191218593D 1 1.00000 0.00000 0
Jmol version 12.3.26 2012-05-19 18:34 EXTRACT: ({0 3 4})
3 2 0 0 0 0 1 V2000
2.89480 4.81990 0.01710 N 0 0 0 0 0 0
3.52580 2.75730 -0.17290 N 0 0 0 0 0 0
3.94370 4.03730 -0.25710 C 0 0 0 0 0 0
1 3 2 0 0 0
2 3 1 0 0 0
M END
end "mol"
select search("$([#7][#6]([#7&!$([#7][O])])=[#7])")
show selected
was returning 1 atom, but should be 0 (because there are only two N atoms!)
bug fix: measurementUnits = "au" does not work
bug fix: select 1.0 fails
bug fix: COMPARE broken
bug fix: Writing file into .jmol file after reading it from another results in the whole
zip file being copied into the new .jmol file.
=============================================================================
version=12.3.25
new feature: MMFF94 single point energy calculation and minimization
set forcefield "MMFF"
checkmm.spt
checkmm "AMHTAR01";minimize energy
AMHTAR01 Initial E = 66.180 kcal/mol # should be 66.18011
checkmm "ARGIND11";minimize energy
ARGIND11 Initial E = -207.436 kcal/mol # should be -207.43598
validation complete. The following 13 structures (of 761) do not validate to within 0.1 kcal/mol
1 COMKAQ E= -7.3250003 Eref= -7.6177 diff= 0.2926998
-- MMFF94 ignores 1 of 5-membered ring torsions for a 1-oxo-2-oxa-bicyclo[3.2.0]heptane
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
2 DUVHUX10 E= 64.759995 Eref= 64.082855 diff= 0.6771393
-- MMFF94 ignores 5-membered ring issue for S-S-containing ring
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
3 FORJIF E= 35.978 Eref= 35.833878 diff= 0.14412308
-- MMFF94 uses some sort of undocumented empirical rule used for 1 torsion not found in tables
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
4 JADLIJ E= 25.104 Eref= 24.7038 diff= 0.4001999
-- ignores 5-membered ring for S (note, however, this is not the case in BODKOU)
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
5 KEPKIZ E= 61.127 Eref= 61.816277 diff= 0.68927765
-- MMFF94 requires empirical rule parameters
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
6 PHOSLA10 E= 111.232994 Eref= 112.07078 diff= 0.8377838
-- MMFF94 ignores all 5-membered ring torsions in ring with P
-- (note, however, this is not the case in CUVGAB)
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
7 PHOSLB10 E= -93.479004 Eref= -92.64081 diff= 0.8381958
-- MMFF94 ignores all 5-membered ring torsions in ring with P
-- (note, however, this is not the case in CUVGAB)
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
empirical-rule-requiring models: (all are nonaromatic heterocycles)
8 ERULE_01 E= -22.582 Eref= -21.515108 diff= 1.0668926
9 ERULE_02 E= 29.407999 Eref= 29.799572 diff= 0.39157295
10 ERULE_03 E= -3.326 Eref= -2.9351802 diff= 0.3908198
11 ERULE_04 E= -2.572 Eref= -2.31007 diff= 0.26193
12 ERULE_07 E= 2.873 Eref= 3.16775 diff= 0.29474998 (fixed in 123.3.26 by correcting angle calc)
13 ERULE_08 E= 33.734 Eref= 34.41382 diff= 0.6798172
bug fix: compare {22-31} {7-16} subset {*.ca} should work without ATOMSET next
bug fix: compare {22-31} {7-16} should work, using {spine} as default
bug fix: isosurface molecular for certain flat models will fail to cap H atoms
bug fix: calculate partial charge fails after model kit changes
(because Bond[] bonds field not cleaned
bug fix: dipole command fails after model kit changes
code: refactoring of minimize for generalization
=============================================================================
version=12.3.24
new feature: SMARTS search for atom type using quotes: ["37"]-["58"]
new feature: SMARTS option /aromaticdouble/ allows distinguishing between aromatic single and double bonds
new feature; SMARTS option /aromaticstrict/ checks 6-electron rule for aromatics
new feature: CALCULATE partialCharge does MMFF94 charge calculation
-- all atom types validated
-- charge values validated to +- 0.001001 over the 761-atom dative validation set
new feature: isosurface CACHE
-- creates a JVXL version of the surface (possibly outside of Jmol, but that's not implemented yet)
-- saved by write JMOL as a JVXL file "isosurface_ID"
(where ID is the original isosurface ID) within the JMOL zip collection
-- Warning! not saved using write SPT
***ALWAYS*** use write JMOL or write PNGJ after using the CACHE option, not write SPT
-- invoked by isosurface file "cache://isosurface_ID"
-- cleared by reset CACHE
-- allows rapid recreation of an isosurface across file loads
-- possibly limited to a subset of surface types
-- not fully tested
new feature: write ... "http://....."
-- POSTs JMOL or IMAGE or structure or whatever to a server as application/octet-stream
-- to be used in Proteopedia for saving a fully self-contained state
new feature: load filter "CENTER" -- centers models on the first model as they are loaded
new feature: load filter "NAME=..." -- loads only those models with a name that contains ...
new feature: calculate partialcharge
-- works on currently selected set of atoms
-- uses MMFF94 charge calculation (unverified; most certainly not quite correct)
-- preliminary only; working on validation
bug fix: x = {"c1": 3}; if(x["c1"]) should return TRUE
code: Simple way to assign MMFF94 atom types and partial charges
-- N,S-containing compounds not validated; CHO-containing compounds partially validated
bug fix: MOL2 reader assuming PDB for non-PDB format files (such as MMFF94-dative.mol2)
bug fix: label %W not working properly for non-PDB files
bug fix: write MOL does not save partial-single bond as type 8 ("ANY")
bug fix: set echo IMAGE fails (since 12.3.20)
code: (applet) JmolCore.js free of need for JSON
=============================================================================
version=12.3.23
new feature: (applet) new interface for Jmol as an HTML object as well as full support on all platforms
using a ChemDoodle fall-back option for Java/Applet-challenged platforms (iPad,iPhone,Android)
Note that Jmol.js is no longer required, but not all of the features of Jmol.js are in place yet
allows Jmol applets to be created on a page with more flexibility and extendability
possibly using infrastructure of ChemDoodle for multiplatform doodlable structures
required/optional libraries (preferably in the following order):
jQuery.min.js -- required for ChemDoodle or any server-based options
gl-matrix-min.js -- required for ChemDoodle option
mousewheel.js -- required for ChemDoodle option
ChemDoodleWeb.js -- required for ChemDoodle option
JmolCore.js -- required
JmolApplet.js -- required
JmolCD.js -- required for ChemDoodle option
JmolApi.js -- required
Allows Jmol-like objects to be displayed on Java-challenged (iPad/iPhone)
or applet-challenged (Android/iPhone) platforms, with automatic switching to
whatever is appropriate. You can specify "ChemDoodle-only", "Jmol-only", "Image-only"
or some combination of those -- and of course, you are free to rewrite the logic below!
Allows ChemDoodle-like 3D and 3D-faked 2D canvases that can load files via a privately hosted
server that delivers raw data files rather than specialized JSON mol data.
Access to iChemLabs server is not required for simple file-reading operations and
database access. PubChem and image services are provided by a server-side PHP program
running JmolData.jar with flags -iR (at St. Olaf College).
For your installation, you should consider putting JmolData.jar and jmolcd.php
on your own server. Nothing more than these two files is needed on the server.
The NCI and RCSB databases are accessed via direct AJAX if available (xhr2).
new feature: PubChem search for name (which can be a CAS number), cid, or SMILES using ":"
from pubChemFormat = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";
(many thanks to Evan Bolton and Paul Thiessen (NIH) for their assistance on this.
load :name:tylenol # or load :tylenol
load :cas:103-90-2 # or load :103-90-2
load :cid:1983 # or load :1983
load :smiles:C/C=C/C
bug fix: callback functions for modular calls: applet0.readCallback(....)
bug fix: Molden reader problems reading frequencies
bug fix: VASP reader with {n n n} and vibration vectors problem
bug fix: in 2bat, SIA was considered part of the carbohydrate chain because we were not checking bonding
=============================================================================
version=12.3.22
new feature: Jmol extensions to ChemDoodle allow display of Jmol, ChemDoodle-equivalent (simple model only),
or just an image with server-side JmolData.jar support.
JmolCD.js -- Jmol ChemDoodle extension author: Bob Hanson, hansonr@stolaf.edu 4/16/2012
requires ChemDoodleWeb.js and ChemDoodleWeb-libs.js
prior to JmolCD.js
allows Jmol applets to be created on a page with more flexibility and extendability
using much of the infrastructure of ChemDoodle.
allows Jmol-like objects to be displayed on Java-challenged (iPad/iPhone)
or applet-challenged (Android/iPhone) platforms, with automatic switching to
whatever is appropriate. You can specify "ChemDoodle-only", "Jmol-only", "Image-only"
or some combination of those -- and of course, you are free to rewrite the logic below!
allows ChemDoodle-like 2D and 3D canvases that can load files via a privately hosted
server that delivers raw data files rather than specialized JSON mol data.
access to iChemLabs server is not required for simple file-reading operations and
database access. Database and image services are provided by a server-side PHP program
running JmolData.jar with flags -iR.
In this case, the NCI and RCSB databases are accessed via a St. Olaf College server,
but for your installation, you should consider putting JmolData.jar and jmolcd.php
on your own server. Nothing more than these two files is needed on the server.
new feature: write CD (simple ChemDoodle JSON format -- atoms and bonds only)
For example: java -jar JmolData.jar -iRJ "load $tylenol;print write('cd')"
generates: {"mol":{"a":[{"x":0.20549999,"y":0.8303,"z":0.3823},{"x":0.6906,"y":-1.4656999,"z":-0.14220001},{"x":1.5485,"y":1.1359,"z":0.2829},{"x":2.0332,"y":-1.1585,"z":-0.24180001},{"x":-3.9799001,"y":-0.1617,"z":0.1295},{"l":"H","x":4.2731,"y":0.35680005,"z":0.7047},{"l":"H","x":-1.8655999,"y":-1.6522,"z":0.6012},{"x":-0.2273,"y":-0.4718,"z":0.17},{"x":2.4650002,"y":0.1425,"z":-0.029099999},{"l":"O","x":-2.1741998,"y":1.1759001,"z":-0.59169996},{"l":"O","x":3.7872,"y":0.4441,"z":-0.1268},{"x":-2.5170999,"y":0.1262,"z":-0.089999996},{"l":"N","x":-1.5898,"y":-0.78279996,"z":0.2712},{"l":"H","x":-0.50740004,"y":1.6029,"z":0.6296},{"l":"H","x":0.35450003,"y":-2.4786,"z":-0.3079},{"l":"H","x":1.8853,"y":2.1487997,"z":0.4477},{"l":"H","x":2.7472,"y":-1.9314001,"z":-0.485},{"l":"H","x":-4.3884,"y":-0.65880007,"z":-0.7504},{"l":"H","x":-4.0964003,"y":-0.8086,"z":0.9991},{"l":"H","x":-4.513,"y":0.7739,"z":0.2986}],"b":[{"b":8,"e":10},{"b":9,"e":11,"o":2},{"b":7,"e":12},{"b":11,"e":12},{"b":0,"e":7,"o":2},{"b":1,"e":7},{"b":0,"e":2},{"b":2,"e":8,"o":2},{"b":3,"e":8},{"b":1,"e":3,"o":2},{"b":4,"e":11},{"b":5,"e":10},{"b":6,"e":12},{"b":0,"e":13},{"b":1,"e":14},{"b":2,"e":15},{"b":3,"e":16},{"b":4,"e":17},{"b":4,"e":18},{"b":4,"e":19}]}}
(this ended up NOT being used in the Jmol extension to ChemDoodle)
new feature: (JmolData) -iR (silent, restricted) mode sends output from PRINT and ECHO commands to SYSOUT
and also restricts the application to no local file read/writing
bug fix: "connect;" command in states saved prior to 11.9.24 and then read by versions after that
The order in which Jmol created bonds changed in 11.9.24. Due to this, Jmol must check for the
version number of Jmol used to create a state, and if it was before this point, it must
apply "legacy" autobonding methods. Unfortunately, if that state from pre-11.9.24 versions
contains the "connect;" command, which it would if someone used the CONNECT command by itself
to regenerate all bonds in a model PRIOR to saving the state (Proteopedia does this), then
those scripts will be misread in versions 11.9.24-12.2.21/12.3.21.
bug fix: antialiasDisplay does not show drag-box properly
bug fix: SMARTS syntax [${xxx}n] and [${xxx}m-n] changed to [$n{xxx}] and [$m-n{xxx}]
to avoid conflict with specifying isotope
=============================================================================
version=12.3.21
new feature: app flag -R restricts file access -- no local file reading; no writing, no logging
// disables WRITE, LOAD file:/, set logFile
// command line -g and -w options ARE available for final writing of image
// for use with headless operation
new feature: app flag -T <seconds> headless timeout delay for "exitJmol"
note: Headless operation with image creation works perfectly using JmolData.jar
java -Djava.awt.headless=true -Xmx512m -jar "JmolData.jar" -RJ "load $tylenol;" -g1000x1000 -wJPG:t.jpg
see also: http://leshazlewood.com/2009/08/26/linux-javaawtheadless-and-the-display-environment-variable/
// determined by GraphicsEnvironment.isHeadless()
// from java -Djava.awt.headless=true
// disables command threading
// disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN <rate>, ANIMATION ON
// turns SPIN <rate> <end> into just ROTATE <end>
new feature: JSpecView JCamp-MOL files can reference model="$xxxx" -- model retrieved from NCI
bug fix: PDB reader
and state scripts created with 12.1.51-12.2.20 and 12.3.0-12.3.20
state scripts prior to those versions with multiple models
and also select BOND commands will read the bond indexes incorrectly
and, in addition, will assign proper CONECT links only to the last model
bug fix: if (....) # comment fails
bug fix: Molden reader hack for bad Molden files with ** instead of atom number in [GTO]
bug fix: headless creation of JPG fails
bug fix: spin .... 30 takes 30 to be number of degrees, not rate
version=12.3.20 -- skipped
=============================================================================
version=12.3.19
new feature: select baseModel for JSpecView
new feature; model {atomset} -- model of first atom in this set
bug fix: set dragSelected disallows popup menu
bug fix: MOPAC (PUBLIC DOMAIN) output reader can fail on reading vibrations
bug fix: Spartan 10 archives have .gz and .carc files. This fix adds .gz reading;
work-around is that Spartan 10 allows saving of Archive without carc compression,
which is a proprietary format. From Wavefunction:
"If you want all files to use the "text" version, you can go to the
Options->Preferences->X-Platform pane and make sure "Use Binary Archive" is unchecked."
bug fix: rotateSelected of models that have had dots at one point retrieved from a state file fails
code: refactored org.jmol.g3d.[Normix3d,Shade3D] --> org.jmol.util.[Normix, Shader]
code: refactored org.jmol.geodesic.Geodesic --> org.jmol.util.Geodesic
bug fix: Jmol defaults not being loaded with startup option -n (no display)
bug fix: UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()
failed for non-graphics system, and even though it is an exception, it
isn't trapped by try/catch.
bug fix: point() function does not accept 3x1 array
bug fix: show x where x is a matrix does not have ',' before tabs, so it can't be clipped directly
back into Jmol
code: better coding for quaternions
=============================================================================
version=12.3.18
new feature: JSpecView reads and displays 2D spectra very quickly -- all
tested JCamp-DX 6.0 files readable. -- JSpecView 2.0.10176
bug fix: allow for alternating list/hash entry:
for example: print getproperty("jspecview","##TITLE")["items"][1]["spectra"][1]["id"]
instead of: print ((getproperty("jspecview","##TITLE")["items"][1])["spectra"][1])["id"]
bug fix: GaussianReader not reading "Natural Orbitals" section from
B3LYP 6-31g sp gfprint pop(full,NO)
bug fix: Jmol support for ZIP collection of JDX files read properly
bug fix: support for file reading with BOM UTF-8, UTF-16, or UTF-32
bug fix: script processor not recognizing UTF-8 Binary Order Mark at start of script
bug fix: (undocumented) POLYHEDRA {...} to {...} with COLOR or TRANSLUCENT fails
bug fix: POLYHEDRA command or COLOR POLYHEDRA can change selection
bug fix: PDB reader doesn't recognize 16 LINK records at start of file
bug fix: script xxxx(xxx)xxx/xx.xxx fails at "(" due to revision 16201 2011-10-02
=============================================================================
version=12.3.17
new feature: (JspecView 2.0.10033) new script commands (indicated with *)
UNKNOWN("?"),
APPLETID("APPLETID"),
APPLETREADYCALLBACKFUNCTIONNAME("APPLETREADYCALLBACKFUNCTIONNAME"),
AUTOINTEGRATE("AUTOINTEGRATE", "TF"),
BACKGROUNDCOLOR("BACKGROUNDCOLOR", "C"),
*CLOSE("CLOSE", "spectrumId or fileName or ALL"),
COMPOUNDMENUON("COMPOUNDMENUON", "TF"),
COORDCALLBACKFUNCTIONNAME("COORDCALLBACKFUNCTIONNAME"),
COORDINATESCOLOR("COORDINATESCOLOR", "C"),
COORDINATESON("COORDINATESON", "TF"),
*DEBUG("DEBUG", "TF"),
DISPLAYFONTNAME("DISPLAYFONTNAME", "fontName"),
ENABLEZOOM("ENABLEZOOM", "TF"),
ENDINDEX("ENDINDEX"),
*EXPORT("EXPORT", "[JPG,PNG,XY,...] \"filename\""),
GETSOLUTIONCOLOR("GETSOLUTIONCOLOR", ""),
GRIDCOLOR("GRIDCOLOR", "C"),
GRIDON("GRIDON", "TF"),
*INTEGRATE("INTEGRATE", ""),
INTEGRALPLOTCOLOR("INTEGRALPLOTCOLOR"),
INTEGRATIONRATIOS("INTEGRATIONRATIOS"),
INTERFACE("INTERFACE"),
*IRMODE("IRMODE", "A or T or ?"),
*LABEL("LABEL", "x y [color and/or \"text\"]"),
*LOAD("LOAD", "[APPEND] \"fileName\""),
MENUON("MENUON"),
OBSCURE("OBSCURE"),
*OVERLAY("OVERLAY", "spectrumID, spectrumID, ..."),
PEAKCALLBACKFUNCTIONNAME("PEAKCALLBACKFUNCTIONNAME"),
PLOTAREACOLOR("PLOTAREACOLOR", "C"),
PLOTCOLOR("PLOTCOLOR", "C"),
PLOTCOLORS("PLOTCOLORS"),
REVERSEPLOT("REVERSEPLOT", "TF"),
SCALECOLOR("SCALECOLOR", "C"),
SPECTRUM("SPECTRUM", "spectrumID"),
SPECTRUMNUMBER("SPECTRUMNUMBER"),
STARTINDEX("STARTINDEX"),
SYNCCALLBACKFUNCTIONNAME("SYNCCALLBACKFUNCTIONNAME"),
SYNCID("SYNCID"),
TITLEBOLDON("TITLEBOLDON", "TF"),
TITLECOLOR("TITLECOLOR", "C"),
TITLEFONTNAME("TITLEFONTNAME", "fontName"),
UNITSCOLOR("UNITSCOLOR", "C"),
VERSION("VERSION"),
XSCALEON("XSCALEON", "TF"),
XUNITSON("XUNITSON", "TF"),
YSCALEON("YSCALEON", "TF"),
YUNITSON("YUNITSON", "TF"),
*ZOOM("ZOOM", "OUT or x1,x2");
new feature: allows simpler color scheme definition
color property occupancy "myscheme=red green blue"
Var x = ["red","green","blue"]; color property occupancy @{"myscheme=" + x}
bug fix: JCampDX reader resolving should allow spaces before "##TITLE"
bug fix: jvxl issue when color PHASE and translucent
-- upon reading JVXL doesn't handle translucency right
-- upon writing SPT doesn't preserve colors
bug fix: user variable lower case "x" not cleared by "X = none"
bug fix: draw HELIX fails for residue numbers < 0
code: better Enum structure using name()
=============================================================================
version=12.3.16
new feature: (application) SYNC ON; sync * "JSpecView:..." sends commands to JSpecView
new feature: (JSpecView) accepts commands using public syncScript(script)
bug fix: GAMESS-US reader error reading NBOs
bug fix: print [2, 3, 4].mul([3,4,5]) fails
bug fix: missing ANISOU records cause file-read error in PDB files
bug fix: JCAMP-DX reading by JSpecView for tiered BLOCK files
=============================================================================
version=12.3.15
new feature: JCAMP-DX file reading
-- reading of ##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview)
new feature: context menu Spectra submenu
new feature: JSpecView integration into Jmol application
-- if model/peak-enhanced JDX file is read, clicking on an atom or switching
to an IR vibration or MS fragment displays the appropriately highlighted spectrum/fragment
new feature: sync ~ 'Select: xxx'
-- xxx can include file="xxx" model="xxx" atoms="xxx" select="xxx" script="xxx"
-- file and model combined as model ID "file#model"
-- will automatically load the file if the given file#model ID is not found
-- atoms = list of atom numbers separated by commas: 1,2,3 --> @1 or @2 or @3
-- select is any valid selection such as THR or 1-30
-- automatically adds "visible &" to atoms or select
-- requires sync ON
new feature: NFF neutral file format reader (http://paulbourke.net/dataformats/nff/nff1.html)
for electron microscopy data exported from IMOD
new feature: preliminary JCAMP-DX file reader, where <models></models> is present
new feature: when picking struts or delete bond or measure, distance shows as per usual measurement
bug fix: SLAB unit cell not showing all lines
bug fix: CRYSTAL reader needs to change to MOLECULAR when X(ANGSTROMS) found (fullerene slab)
bug fix: Popup Menu item hbond calculate should not require PDB
=============================================================================
version=12.3.14
bug fix: state after frame RANGE or frame 0 not saved properly (state saves "frame all" instead of "frame 0")
bug fix: frame n does not work properly after load APPEND
bug fix: measurement units may appear as full word "nanometers" instead of "nm"
bug fix: user bindings do not access _atomPicked
-- solution is to add _ATOM _BOND _POINT _OBJECT to user binding actions
=============================================================================
version=12.3.13
new feature: isosurface SCALE extends to volume file readers
new feature: zoom $isosurface1 0 -- scales to match isosurface boundbox
bug fix: getProperty("bondinfo",[{13}]) gets info for atom 13 instead of bond 13
bug fix: isosurface offset does not change boundbox or zoom/center points
note to Bob: jpe needs update of img/blank.js js/top_buttons.js htm1/quickvs.js,qv_msgs.js molview/JmolAppletSigned.jar
=============================================================================
version=12.3.12
bug fix: symmetry popup submenu not enabled
bug fix: show spacegroup not working
bug fix: lcaocartoon for allene central carbon py incorrect
bug fix: antialiasdisplay (and image writing) not compatible with scaleAngstromsPerInch
bug fix: last group of protein cartoon will not display if it is not helix and not sheet
bug fix: getproperty MENU does not work
bug fix: PDB reader of multiple-bond files with duplicated bonds does not ignore duplicate
=============================================================================
version=12.3.11
new feature: plot ramachandran -- now those points .phi and psi return values
-- load 1crn.pdb;plot ramachandran;print {2.1}.psi
new feature: LOAD .... filter "reverseModels"
-- does just that
-- for IRC calculation transition state -> minimum reversal
new feature: measures "2:%VALUE %UNITS//xx"
-- where xx is a specified unit such as nm or Angstroms
-- overrides set measurementUnits
-- fixes state problem when units or labels are changed after measurements are made
-- operates on selected measurements only (or all, if no measurements are selected)
bug fix: frame 0 during animation can cause exception
bug fix: changes in defaultDistanceLabel not always preserved in state correctly
bug fix: parameters can be set to invalid values using xxx = ... instead of set xxx ...
bug fix: (Application) proper Edit...Preferences dialog action
=============================================================================
version=12.3.10
new feature: _animTimeSec
new feature: Application -- press and hold animation next/prev button to continuously run animation
new feature: write PDB adds CONECT records
-- for all multiple bonding and all HETATM bonds
-- uses CONECT i j j to indicate multiple bonding
new feature: compare {from} {to} FRAME
-- aligns frames automatically
-- particularly nice for IRC calculation animations
-- for example: compare {file=2} {1.1} FRAME
-- can be followed by quaternion, atom, or SMILES options
-- for example: compare {file=2} {1.1} FRAME ATOMS @1 @5 @2 @8 @3 @9
(all of file 2 atoms moved) file 2 atoms 1,2,3 aligned
with file 1.1 atoms 5,8,9)
-- if {to} is a subset of {from}, then FRAME is unnecessary,
and if ATOMS is included, then just the list of alignment
atoms is necessary. For example:
compare {*} {1.1}
compare {*} {1.1} atoms @1 @2 @3
-- see http://chemapps.stolaf.edu/jmol/docs/examples-12/mp for more examples
bug fix: script @{x} fails
bug fix: Molecular Playground should allow for set allowGestures OFF to disallow swipe
bug fix: lcaoCartoon dual color p orbitals giving white for one lobe
new feature: set echo myecho SCALE 0.3 -- for image scaling
bug fix: after "ZAP; LOAD append" show orientation will have incorrect zyz script
bug fix: function call with @x or @1 in parameters fails
bug fix: PNGJ reading remote fails
bug fix: H5T should not be used as a lead atom ever, because of set showHydrogens FALSE
bug fix: adding H atoms to mol2 file faulty
bug fix: load xxx.png;write PNGJ xxx.png (to same file as loaded) fails
=============================================================================
version=12.3.9
new feature: FRAME DELAY x.y
-- specific delay (in seconds) in animation at a given frame
-- applies to all currently in-frame models
bug fix: set isKiosk should:
(a) not be reversible
(b) not allow file saves other than logging
(c) not allow prompt dialogs
(d) not allow console or popup menu or ScriptEditor
bug fix: background colors saved to state can be off very slightly
bug fix: draw PLANE with three vertices problems after save -- four-atom planes, not three
bug fix: x = file("?") fails on Cancel
bug fix: delay not allowed within try{...}
=============================================================================
version=12.3.8
new feature: MolecularPlayground -- remote status and remote control
-- see for example http://chemapps.stolaf.edu/jmol/mpstatus.php
-- set topic, subtopic, delay from a web page
-- set banner and image for website from Jmol
new feature: load("http://.....?POST?_PNG_") or load("http://....?POST?_PNGJ_")
-- sends PNG or PNGJ image to server
-- return value is whatever server is set up to send
-- used by MolecularPlayground at St. Olaf to send current state to web server
new feature: polyhedra FULLYLIT -- useful for zeolites along with COLLAPSED
new feature: ZMATRIX upgraded to allow all forms of Gaussian input
http://www.gaussian.com/g_tech/g_ur/c_zmat.htm
bug fix: set picking DRAW does not work on polygon sets
bug fix: set picking DRAW does not report position change
bug fix: MPJmolApp (Molecular Playground) problems when navigation is on
bug fix: CifReader (molecular type, with GEOM_BOND records) adds
extra atoms when embedded in JMOL or PNGJ file or part load FILES command
bug fix: PdbReader -- crystallographic non-PDB files not checking special positions
=============================================================================
version=12.3.7
new feature: "Write PNG+JMOL" added to application and signed applet menu
code: dispensing with InputStream in favor of BufferedInputStream
new feature: write PNGJ
-- creates a PNG file with appended JMOL (zip) data containing
all necessary files, MANIFEST, and script file.
-- viewable in directories as an "icon" and readable by image readers
-- draggable back into Jmol and readable using LOAD
-- PNG file includes:
-- iTXt field "Jmol Type\0PNGJxxxxxxxxx+yyyyyyyyy"
where xxxxxxxxx is a pointer to the ZIP data
yyyyyyyyy is the number of ZIP data bytes
-- iTXt field "Software\0Jmol 12.3.7 2011-10-11 15:30"
-- iTXt field "Creation Time\0Tue, 24 Nov 2011 19:56:10 -0600"
-- yyyyyyyyy bytes of .JMOL zip data
-- show FILE "xxx.PNG" will show list of contained files.
-- show state FILE "xxx.PNG" will extract state
-- show FILE "xxx.PNG|1crn.pdb" for example will extract file
new feature: simple Z-Matrix reader
-- invoked by ZMATRIX:: or file starting with #ZMATRIX
-- lines starting with # are comments, which can contain jmolscript:
-- blank lines are ignored
#ZMATRIX -- methane
C
H 1 1.089000
H 1 1.089000 2 109.4710
H 1 1.089000 2 109.4710 3 120.0000
H 1 1.089000 2 109.4710 3 -120.0000
-- allows bond order specification
#ZMATRIX -- CO2
C
O 1 1.3000 2
O 1 1.3000 2 180 2
-- any position number may be replaced by a unique atom name, with number:
#ZMATRIX -- CO2
C1
O1 C1 1.3000 2
O2 C1 1.3000 O1 180 2
-- allows for dummy atoms Xn, allowing for positioning:
#ZMATRIX -- CO2
X1
X2 X1 1.0
C1 X1 1.0 X2 90
O1 C1 1.3000 X2 90 X1 0 2
O2 C1 1.3000 O1 180 X2 0 2
-- negative distance indicates that the second angle is a normal angle, not a dihedral
#ZMATRIX -- NH3 (using simple angles only)
N1
H1 N1 1.0
H2 N1 1.0 H1 107
H3 N1 -1.0 H1 107 H2 107
-- negative distance and one negative angle reverses the chirality
#ZMATRIX -- NH3 (using simple angles only; reversed chirality)
N1
H1 N1 1.0
H2 N1 1.0 H1 107
H3 N1 -1.0 H1 -107 H2 107
-- symbolics may be used -- they may be listed first or last
#ZMATRIX
dist 1.0
angle 107
N1
H1 N1 dist
H2 N1 dist H1 angle
H3 N1 -dist H1 angle H2 angle
-- If #ZMATRIX is not the start of the file, MOPAC style is assumed.
The first two lines will be considered to be comments and ignored:
AM1
Ethane
C
C 1 r21
H 2 r32 1 a321
H 2 r32 1 a321 3 d4213
H 2 r32 1 a321 3 -d4213
H 1 r32 2 a321 3 60.
H 1 r32 2 a321 3 180.
H 1 r32 2 a321 3 d300
r21 1.5
r32 1.1
a321 109.5
d4213 120.0
d300 300.0
bug fix: show orientation shows incorrect zyz format if reset uses file-based orientation matrix (smol, Sygress)
bug fix: isosurface plane xy map mep
code: MPJmolApp work
bug fix: user variables should not be rest by INITIALIZE in an spt file
bug fix: x3d/vrml outputting unnecessary spheres
-- bond caps within opaque atoms removed (not precisely correct to do that)
bug fix: minimization broken
bug fix: contact still not quite right -- setting default to +0.0 instead of +0.25
=============================================================================
version=12.3.6
new feature: load files "xxx.tlsout" "xxxx.pdb"
-- loads REFMAC-style TLS data into xxxx.pdb
new feature: contact SASURFACE <radius>
-- ignores solvent (as does CAP)
bug fix: contact command hbond/clash cutoff not sensitive to H-O/N vs O/N-O/N
-- set to -1.2 for H-N/O, -1.0 for N/O-N/O
bug fix: contact command default probe radius should be 0.0 except for VDW (0.25)
bug fix: minimize constraint CLEAR broken
bug fix: constraints not reported in show minimization
bug fix: set measures off broken
bug fix: contact color density broken
bug fix: contact volume report not correct for color density
bug fix: MO HOMO not set properly when using LUMO = "lowest E > 0" (GAMESS-US reader)
bug fix: zSlab settings not stored properly in parameters; should have default zSlab = 50
=============================================================================
version=12.3.5
new feature: color isosurface PHASE color1 color2
-- allows post-isosurface creation coloring by phase (atomicOrbitals)
bug fix: isosurface scale 0.5 plane... broken if no atoms present
bug fix: isosurface color density broken
bug fix: set PdbAddHydrogens does not transfer C atomSymmetry to H atoms
bug fix: contact() function not working when typed from console
bug fix: set axesOrientationRasmol not working properly (since 11.5.51)
code: org.jmol.modelsetbio.BioModel localizes more bio-only code into modelsetbio package
code: removal of org.jmol.modelset.Polymer
code: refactoring and organizing RepaintManager and ShapeManager
=============================================================================
version=12.3.4
bug fix: frame x.y - y.z not working
bug fix: with antialiasDisplay, dragMolecule goes 1/2 speed of cursor
bug fix: nucleic acid residues with HO5' may render last group strangely (since 12.0.RC16, 6/6/2010)
bug fix: workaround for weird Mac Point3i(Point3i pt) class initializer bug
bug fix: array.bin(low,high,binSize) not documented and can cause exception
bug fix: MO readers can fail if inappropriate filter "TLS" is given
bug fix: PDB TLS error reading TLS data missing "NUMBER OF COMPONENTS" line
=============================================================================
version=12.3.3
new feature: ellipsoid SET 1; ellipsoid SET 2;
-- TLS ellipsoids are dual
-- TLS-S is SET 1; TLS-T is SET 2
-- after issuing this command, further size or color commands affect only that set
-- needs verification by Ethan Merrit
new feature: load xxx.pdb filter "TLS" -- loads TLS data
new feature: atom property property_tlsGroup
new feature: MolecularPlayground now accepts messages to the banner:
message banner: xxxxxxx
new feature: MolecularPlayground fully functional.
This application (MPJmolApp) is part of a three-part suite
that runs on a Mac mini involving:
"Hub" [name] for overall control (Mac app; not open source yet)
MPKinectDriver for obtaining motion events (Mac app; not open source yet)
MPJmolApp for displaying the results (source here)
The Hub and MPJmolApp communicate over local port 31416, sending
JSON messages back and forth. (See note in org.jmol.app.jsonkiosk.JsonNioService.java)
For demonstrations of the installation at St. Olaf College,
see the following YouTube videos:
http://www.youtube.com/watch?v=iQRkuku8ry0
http://www.youtube.com/watch?v=XCRrRZe1j6g
http://www.youtube.com/watch?v=FTTIVWGtFD0
For details relating to the original Molecular Playground
installation at U. Mass.-Amherst, see
http://molecularPlayground.org
Note that all of the functionality of the original MP are
present in MPJmolApp
new feature: MolecularPLayground can now ignore all Hub requests for
commands and content changes, thus allowing its own configuration
script to drive the presentation instead of the Hub's. So the Hub
can be used simply as an interface to the Kinect driver. This just
allows a simpler development interface -- a simple three-column Excel file can
be used to drive a presentation. (see org.jmol.molecularplayground.biophysics.xlsx)
-- MPJmolApp looks for the file MpJmolAppConfig.spt
-- This file can override MPJmolApp's default parameters:
NIOContentPath
-- default: System.getProperty("user.dir").replace('\\', '/')
+ "/Content-Cache/%ID%/%ID%.json"
-- ignored if NIOcontentDisabled ends up true (see below)
NIOterminatorMessage
-- default: "MP_DONE"
NIObannerEnabled
-- default: true
NIOcontentScript
-- default: (not present, setting NIOcontentDisabled=false)
NIOcontentDisabled
-- default: true if NIOcontentScript is present; false if not
NIOmotionDisabled
-- default: false
-- The script in MpJmolAppConfig.spt is run, along with whatever
default settings are generated by the above checks.
-- Parameters are set by querying the Viewer for those Jmol variables.
-- If NIOcontentDisabled is true, then all JSON messages from the Hub
of types "content", "command", and "banner" are ignored. It is still
important that the running script send "MP_DONE" messages periodically
(within every 6 minutes) so that the Hub knows that MPJmolApp is still
alive and does not try to restart it.
-- If NIOmotionDisabled is true, then all JSON messages from the Hub
of types "move", "sync", and "touch" are ignored.
-- These are checked every time a JSON command is received, so the
running script can specifically turn off motion detection if that
or content detection if that is desired.
-- Note that MPJmolApp has a full console and menu that are available
on the operator's screen, (which is just mirrored to the projector).
This allows for parameter setting and adjustments on the fly.
new feature: show NMR
-- predicted NMR spectrum
-- uses http://www.nmrdb.org/predictor?smiles=xxxx
-- requires NCI SMILES due to bug at nmrdb not allowing "."
bug fix: CRYSTAL reader not properly setting model properties
bug fix: userFunction(x,@y) should operate as per all math
-- parens - value of variable pointed to by y
-- x = myfunc(x, @y) same action as just myfunc(x, @y)
bug fix: userFunction x @y
-- no parens - should operate as value of x and value of y
-- @ is unnecessary but allowed
bug fix: set echo "myecho" [10 10%] not working
bug fix: apiPlatform not correctly accessed in JpegEncoder
bug fix: reading of JVXL files for color density fails to color properly
bug fix: .... vdw 100.0% --- should be OK with float there, even if it rounds.
code: refactored for Molecular Playground and Jmol Android
-- several System.out. messages present.
code: refactoring adapter XML readers
=============================================================================
version=12.3.2
new feature: compare("XXX","XXXX","ISOMER") comparison now includes "AMBIGUOUS STEREOCHEMISTRY!"
new feature: show chemical XXXXX where XXXXX is any NCI Cactus information token:
stdinchikey Standard InChIKey
stdinchi Standard InChI
smiles SMILES
ficts FICTS Identifier
ficus FICuS Identifier
uuuuu uuuuu Identifier
hashisy Cactvs HASHISY
sdf SD File
names Names
iupac_name IUPAC Name
cas CAS Registry Number(s)
chemspider_id ChemSpider ID
mw Molecular Weight
formula Chemical Formula
h_bond_donor_count Number of Hydrogen Bond Donors
h_bond_acceptor_count Number of Hydrogen Bond Acceptors
h_bond_center_count Number of Hydrogen Bond Acceptors and Donors
rule_of_5_violation_count Number of Rule of 5 Violations
rotor_count Number of Freely Rotatable Bonds
effective_rotor_count Number of Effectively Rotatable Bonds
ring_count Number of Rings
ringsys_count Number of Ring Systems
bug fix: array.bin(low,high,binSize) not documented and can cause exception
new feature: PQR write option
bug fix: load append twice can cause zap to be in wrong place in state file
bug fix: for (x IN {*}) ... makes x a bitset and leads to array[1] for x.atomName
bug fix: for (x IN {*}.bonds) does not work
bug fix: POV-Ray export of cartoons broken
bug fix: script javascript:xxxx() broken
new feature: set vectorSymmetry -- displays vibration vectors as double-ended arrows.
bug fix: SMILES comparison when the number of stereocenters is not the same is wrong
code: popup/modelkit refactoring to isolate awt/Swing references
bug fix: connection deletion removes all measurements -- can't imagine why...
code: JmolModelKitInterface part of apiPlatform call
code: JmolPromptInterface replaced with apiPlatform call
=============================================================================
version=12.3.1
new feature: CASTEP reader (take 2)
-- reads Mulliken files by default, Hirshfield with filter "CHARGE=HIRSH"
-- reads spins into {*}.property_spin. label is %[property_spin]
-- reads Born charge tensors as atom ellipsoids
bug fix: H2,H3 connected to terminal N of protein not backbone
bug fix: select PROTEIN selects non-PDB atoms
bug fix: Molden reader does not read "Sym=X" (missing space after '=')
bug fix: Molden reader does not read angstrom units
bug fix: color isosurface {atomset} <color> does not work if isosurface has not already been mapped.
bug fix: PDB reader not reading Rasmol-style files with multiple bonding
CONECT 1 2 2
or
CONECT 1 2
CONECT 1 2
means for Rasmol double bond between atoms 1 and 2
code: experimenting with fragmentation of applet core classes into _1b, _1c, _1d, _1e, _1f
version=12.3.0
October 4, 2011
