Happy to report the release of Jmol 14.0
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 (
http://www.math.ucsd.edu/~sbuss/ResearchWeb/spheremean/)
new feature: print quaternion([array of quaternions], true)
-- returns standard deviation for spherical mean a la Buss and Fillmore (
http://www.math.ucsd.edu/~sbuss/ResearchWeb/spheremean/)
-- 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
new 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: list = compare({atomset1} {atomset2} SmartsString "BONDS")
new feature: write JSON xxx.json
new feature: [#210] JSON {"mol":...} reader
-- example (penicillin; no actual line breaks)
{"mol":{
"_is2D":false,
"_scale":{"x":1,"y":1,"z":1},
"a":[{"x":3.9236999,"y":-0.9222,"z":0.1835},{"x":3.2479,"y":-3.2106004,"z":0.3821},{"x":5.1731,"y":-1.3284999,"z":-0.24640003},{"x":4.4973,"y":-3.6169,"z":-0.0478},{"x":5.4598002,"y":-2.6759,"z":-0.3623},{"x":1.599,"y":-1.4203,"z":0.9663},{"x":-4.2137,"y":0.8188001,"z":2.5929},{"x":-5.7525997,"y":0.1604,"z":0.70350003},{"l":"H","x":-0.92130005,"y":-0.6858,"z":0.8503},{"x":2.961,"y":-1.8632,"z":0.49760002},{"l":"O","x":-4.989,"y":2.5026002,"z":-1.2333001},{"l":"O","x":-1.2756001,"y":1.6640999,"z":-1.9360001},{"l":"O","x":1.104,"y":-1.4738001,"z":-1.3405999},{"l":"O","x":-4.604,"y":3.4702,"z":0.7158},{"x":-4.4305005,"y":2.47,"z":-0.1623},{"x":0.68810004,"y":-1.2541,"z":-0.2227},{"x":-3.5391,"y":1.3063,"z":0.1875},{"x":-1.4742,"y":-0.7,"z":-1.1997},{"x":-1.8847001,"y":0.7218999,"z":-1.4753001},{"l":"H","x":-5.185,"y":4.1949,"z":0.44660002},{"l":"N","x":-0.5887,"y":-0.86149997,"z":-0.043799996},{"x":-2.9578,"y":-0.84800005,"z":-0.8823999},{"x":-4.298,"y":0.3443,"z":1.1408},{"l":"S","x":-3.3189998,"y":-1.1949,"z":0.8809},{"l":"N","x":-3.159,"y":0.59889996,"z":-1.0386},{"l":"H","x":-2.6423,"y":1.6747,"z":0.6855},{"l":"H","x":-3.5207,"y":-1.4693998,"z":-1.5789001},{"l":"H","x":-4.6569,"y":1.8111,"z":2.6771998},{"l":"H","x":-4.7551003,"y":0.123500004,"z":3.2344003},{"l":"H","x":-3.1692,"y":0.86,"z":2.9017},{"l":"H","x":-5.7794,"y":-0.2569,"z":-0.3031},{"l":"H","x":-6.2558002,"y":-0.5187,"z":1.3918},{"l":"H","x":-6.2588997,"y":1.1256,"z":0.71029997},{"l":"H","x":-1.1443,"y":-1.2523,"z":-2.0796},{"l":"H","x":1.1846,"y":-2.1707997,"z":1.6393999},{"l":"H","x":1.6871,"y":-0.46960002,"z":1.4921},{"l":"H","x":3.7012,"y":0.1303,"z":0.2784},{"l":"H","x":2.4957001,"y":-3.9457002,"z":0.62750006},{"l":"H","x":5.9251003,"y":-0.5933,"z":-0.4921},{"l":"H","x":4.7215,"y":-4.6695,"z":-0.13759999},{"l":"H","x":6.4357004,"y":-2.9933,"z":-0.6989}],
"b":[{"b":10,"e":14,"o":2},{"b":13,"e":14},{"b":14,"e":16},{"b":16,"e":24},{"b":16,"e":22},{"b":21,"e":24},{"b":18,"e":24},{"b":6,"e":22},{"b":7,"e":22},{"b":22,"e":23},{"b":21,"e":23},{"b":17,"e":21},{"b":17,"e":18},{"b":11,"e":18,"o":2},{"b":17,"e":20},{"b":15,"e":20},{"b":5,"e":15},{"b":12,"e":15,"o":2},{"b":5,"e":9},{"b":0,"e":9,"o":2},{"b":1,"e":9},{"b":0,"e":2},{"b":1,"e":3,"o":2},{"b":2,"e":4,"o":2},{"b":3,"e":4},{"b":13,"e":19},{"b":16,"e":25},{"b":21,"e":26},{"b":6,"e":27},{"b":6,"e":28},{"b":6,"e":29},{"b":7,"e":30},{"b":7,"e":31},{"b":7,"e":32},{"b":17,"e":33},{"b":8,"e":20},{"b":5,"e":34},{"b":5,"e":35},{"b":0,"e":36},{"b":1,"e":37},{"b":2,"e":38},{"b":3,"e":39},{"b":4,"e":40}]
}}
-- is2D will trigger minimization
-- scale indicates overall scaling present in the "a" records
new 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: 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 = '<space>'
new feature: new propertyColorScheme "friendly"
-- color-blindness-friendly color scheme
-- used at RCSD
-- example:
set propertyColorScheme "friendly"
color {chainNo > 0} property chainNo
new feature: JSpecView completely Java-free; includes 2D nmr and PDF
printing of spectra
new feature: WRITE PDF <width> <height> <quality> "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
--
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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