Commit [r18178] Maximize Restore History

for release: ___JmolVersion="13.1.15"

FEATURE CHANGE: default JPEG quality set to 100 (was 75, which looks crappy)

new feature: select command parameter completion using [TAB] includes variables

new feature: PyMOL-like label offset options:

set labelOffset [sx, sy, sz]
set labelOffset [mode, sx, sy, sz, ax, ay, az]


sx,sy,sz are screen coord offsets
-- in Angstroms
-- applied after view rotation
-- sy > 0 LOWERS label
ax,ay,az are xyz position (in Angstroms; applied before view rotation)
mode == 1 indicates xyz position is an offset to the atom position
mode != 1 indicates xyz position is absolute

new feature: CASTEP energy reading
new feature: XCrysDen file reader
new feature: VASP POSCAR reader

new feature: set cartoonLadder -- no bases, like PyMOL

new feature: model CREATE n
-- allows "empty" model creation without atoms
-- n = number of models to create
-- defaults to 1

new feature: "all frames" toolbar button starts/stops PyMOL movies: if(_isMovie){if (_animating) {animation off}else{animation play}} else {frame *}

new feature: Jmol/JmolData application -I flag accepts input from and command piping:

type t.spt | jmol -I start Jmol with this script

Note: if you use a pipe, be sure to make "exitJmol" the last command of the script

Add -o for output to System.out. Without the pipe, we are going to control Jmol
from a Jmol> prompt on the command line console

jmol -Io see messages on input console
...messages from Jmol
Jmol> background red;load 1crn.pdb;....
...messages from Jmol
Jmol> exitJmol

Add -n for headless operation (will not exit automatically).

type t.spt | jmol -Ion

Note: if you use a pipe, be sure to make "exitJmol" the last command of the script

Add -i for silent operation (no writing to System.output).

new feature: dots IGNORE {atom set} ON;

new feature: Jmol or JmolData with -g0x0 and load filter "DORESIZE" will automatically
resize the image to what is given in the PyMOL file as its default size:

JmolData -ns "load t.pse filter 'DORESIZE'" -g0x0 -w "PNGJ:t.png"

TODO: PyMOL electron density map data itself (meshes are done)
TODO: PyMOL CGOs as CGO command -- preliminary only
TODO: Jmol's molecular surface renderer not removing inner surface correctly in some cases
TODO: PyMOL movies

bug fix: isosurface map property may not reference correct atom
bug fix: set isosurfacekey may not work with slabbing
bug fix: deleting atoms does not remove bioshape rendering
bug fix: isosurface in multi-model context saved in state with wrong model number
bug fix: PyMOL label fix, including fonts
bug fix: PyMOL rockets, nucleic acid rendering
bug fix: write JPG not working in JavaScript
bug fix: isosurface ... map property colors not cleared entirely before next mapping
bug fix: MSMS reader broken
bug fix: labels lost upon z-shading
bug fix: isosurface property temperature default smoothing broken in 13.1.13.
bug fix: {xxx}.cartoon = {xxx}.temperature.all fails to use correct values (also backbone, trace, etc.)
bug fix: isosurface translucent level not re-zeroed properly
bug fix: IDTF exporter with translucency fails
bug fix: commands f.sort() and f.reverse() fail.
bug fix: {;...;} syntax does not work in 13.1
bug fix: select dots > 0 does not work
bug fix: JmolData broken

code: PyMOL work; CGO command and class CGO extends DRAW preliminary only; preliminary putty; fix for putty+sticks issue
code: PyMOL reader localSettings
code: PyMOL putty hack for Cover1.pse removed; colix index error fixed
code: PyMOL slab and depth; better field of view; even better zslab/zdepth
code: PyMOL reader "backbone" (really a trace -- fixed width?)
code: PyMOL reader isosurface solvent
code: PyMOL reader and full surfaces, mixed bigEndian/littleEndian Pickle reading
code: PyMOL reader: cartoon_ladder_mode approximation as cartoons
code: PyMOL reader: includes cartoon type 1,4,7 -> trace
code: String JmolViewer.runScript(String script) runs script immediately and returns output buffer
code: continued work on PyMOL PSE file reader
code: simplification of JmolViewer interface and access to global parameters:

// several; methods were deprecated and removed in 13.1.15. All are accessible via "getXxxx" methods:

abstract public float getFloat(int tok);
abstract public int getInt(int tok);
abstract public boolean getBoolean(int tok);

//abstract public int getAnimationFps(); see getInt(T.animationFps)
//abstract public boolean getShowHydrogens(); see getBoolean(T.showhydrogens)
//abstract public boolean getShowMeasurements(); see getBoolean(T.showmeasurements)
//abstract public boolean getAxesOrientationRasmol(); see getBoolean(T.axesorientationrasmol)
//abstract public int getPercentVdwAtom(); see getInt(T.percentvdwatom)
//abstract public boolean getAutoBond(); see getBoolean(T.autobond))
//abstract public boolean showModelSetDownload(); deprecated -- was just "true"

hansonr 2013-04-28

changed /trunk/Jmol/src/org/jmol/viewer/
changed /trunk/Jmol/appletweb/
/trunk/Jmol/src/org/jmol/viewer/ Diff Switch to side-by-side view
/trunk/Jmol/appletweb/ Diff Switch to side-by-side view