Thank you, Nico, for releasing Jmol 13.0.15 and 13.1.15. JSmol 13.1.15 is
also released. Some new features here, as well as some mostly minor bug
fixes.*
*
FEATURE CHANGE: default JPEG quality set to 100 (was 75, which looks crappy)
*New Features*
Most of the new features relate to developing compatibility with PyMOL.
This is a fast-moving ongoing project that can be followed at
http://ispcsrv3.weizmann.ac.il/a2jmolb/browse . We are adding more PyMOL
PSE file reading capabilities every day. Please do send us files that we
can test and display.
new feature: PyMOL-like label offset options:
set labelOffset [sx, sy, sz]
set labelOffset [mode, sx, sy, sz, ax, ay, az]
where
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 (like an ECHO, but attached
to an atom's visibility and selectability)
new feature: set cartoonLadder -- default TRUE (standard Jmol rendering of
nucleic acids), but when FALSE no bases, just "ladders", like PyMOL
new feature: model CREATE n
-- allows "empty" model creation without atoms
-- n = number of models to create
-- defaults to 1
new feature: dots IGNORE {atom set} ON; -- allows PyMOL-like dot
representation for selected atoms while totally ignoring specific other
atoms.
new feature: CASTEP energy reading
new feature: XCrysDen file reader
new feature: VASP POSCAR reader
*new application interface features:
*
new feature: select command parameter completion using [TAB] includes
variables
new feature: Jmol application "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 System.in
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: 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"
*bug fixes
*
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: write JPG not working in JavaScript
bug fix: isosurface ... map property colors not cleared entirely before
next mapping
bug fix: MSMS surface 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
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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