Jmol 13.1.16 contains many new features and several bug fixes. It will be
particularly of interest to those who use PyMOL.
JmolVersion="13.1.16"
new feature: color BALLS
-- distinct from color ATOMS because it doesn't get inherited
-- for PyMOL compatibility with sphere_color
new feature: restore SCENE "xxxx" nSec
new feature: Scene menu
-- PyMOL scene names, in order
new feature: added parameters to moveTo allows setting cameraDepth,
cameraX, and cameraY
new feature: moveTo <nseconds> PYMOL [18-element standard PyMOL view matrix]
-- used for PSE file loading
-- to be used also for scenes
[0-8] are 3x3 rotation matrix (row/column inverted)
[9,10] are x,y translations (y negative)
[11] is distance from camera to center (negative)
[12-14] are rotation center coords
[15-16] are slab and depth distance from camera (0 to ignore)
[17] is field of view; positive for orthographic projection
new feature: cache CLEAR
-- same as cache REMOVE ALL
new feature: load xxx.pse FILTER "DOCACHE"
-- specifically for editing large PSE files when included in a state
-- caches streamlined file that is still readable by PyMOL (needs
testing!)
(no electron density map data, for instance -- see HupA_2.pse)
-- caches all isosurfaces, creating JVXL equivalents
-- should be followed with WRITE xxx.pngj or WRITE xxx.jmol or WRITE
xxx.zip
-- for example:
before:
04/07/2013 07:46 AM 11,929,507 HupA_2.pse
$ zap;load SYNC "file:///C:/temp/downloads/HupA_2.pse" filter 'DOcache'
$ write t.zip
after:
Listing archive: t.zip
Physical Size = 395174
Date Time Attr Size Compressed Name
------------------- ----- ------------ ------------
------------------------
2013-05-17 06:46:36 ..... 1092432 219718 HupA_2.pse
2013-05-17 06:46:36 ..... 1473760 6589
isosurface_level2
2013-05-17 06:46:36 ..... 25495 11624 state.spt
2013-05-17 06:46:36 ..... 134 119
JmolManifest.txt
2013-05-17 06:46:36 ..... 0 2
Jmol_version_13.1.16_dev_2013.05.17__2013-05-15_07.09
2013-05-17 06:46:36 ..... 158082 156316 preview.png
------------------- ----- ------------ ------------
------------------------
2749903 394368 6 files, 0
folders
new feature: anim FRAMES [1, 3, 9, 9, 9, 3, 1]
-- arbitrary PyMOL-like model list
new feature: FRAME n
-- same as MODEL n, unless we have PyMOL-like frames
-- if have frames, then FRAME 2 goes to the second frame (model 3 in this
case)
-- MODEL n still always goes to a specific model.
-- all relative options -- FIRST LAST PREV NEXT -- refer to frames if
there are frames
even if the MODEL command is given.
new feature: pyMOL PSE state options: LOAD "FOO.PSE" state FILTER "xxxx"
-- [state not present; default] load all PyMOL states (one PyMOL state ==
one Jmol model)
-- state = 0 (load only the current PyMOL state)
-- state > 0 (load just a specific PyMOL state)
-- FILTER "nosurface" -- load PyMOL file without surfaces
-- FILTER "
new feature: getProperty BONDINFO {atomset1} {atomset2}
new feature: measurements with IDs and radius/diameter:
-- measure ID "xxx" ...
-- measure ID "xxx" RADIUS x.y (or DIAMETER x.y)
-- renders as dots
new feature: set zoomHeight
-- FALSE by default
-- set TRUE for PyMOL-like resizing (scale only set by height
adjustment)
new feature: isosurface color density (decimal)
- variable decimal point size
new feature: PyMOL CGOs as CGO command
- needs testing
- CGO ID "xxx" [ cgo data (float array) ]
- includes basic CGO methods
BEGIN
GL_POINTS
GL_LINES
GL_LINESTRIP
GL_TRIANGLE
GL_TRIANGLE_STRIP
GL_TRIANGLE_FAN
VERTEX
END
COLOR
NORMAL
SIMPLE_LINE
SAUSAGE
TRICOLOR_TRIANGLE
popup: added menu for MEP range -0.1 0.1
PyMOL: uniqueBondSettings working
PyMOL: better scene restore;
PyMOL: adds SASURFACE option (surface_solvent ON), with "carving"
(ProFusion_ABL.pse, scene F6)
PyMOL: abstraction of scene setting from reader
PyMOL: first phase of reader development complete (working with Jaime
Prilusky)
-- 104 test models http://ispcsrv3.weizmann.ac.il/a2jmolb/browse
-- implementation of standard objects, including:
-- atoms with labels
-- bonds
-- standard PyMOL rendering, including:
-- lines
-- sticks
-- nonbonded (stars)
-- nb_spheres
-- cartoons of various types (not plank)
-- rockets
-- ribbon (backbone/trace)
-- putty (trace)
-- dots
-- measures
-- simple CGO objects
-- molecular surfaces
-- electron density as points and meshes
-- custom colors
-- fog and slab
-- morphing movies
-- JVXL caching of isosurfaces
PyMOL: measurement font/offsets enabled
-- adds measure ID "xxx" FONT scale face style
-- adds measure ID "xxx" OFFSET [mode, sx, sy, sz, ax, ay, az]
-- adds measure ID "xxx" OFFSET {sx, sy, sz}
PyMOL: perspective fix for translated center -- H115W.PinM.PSE
bug fix: JavaScript: adding SYNC
bug fix: antialiasing or resizing stray lines problem solved (introduced in
11.0, 08/2006!)
bug fix: "display add" by itself should not do anything
bug fix: Hall translation initialization problem
bug fix: JavaScript reading of old-style JVXL files
bug fix: Gaussian reader not splitting MO set by model
bug fix: polyhedron reading from state
bug fix: connect delete not saved in state
bug fix: rockets not working for alpha polymer (also in 13.0.16)
bug fix: GXL added to carbohydrates
bug fix: show state/anim turns "anim" into "animation"
bug fix: MoldenReader orbitals are not in energy order; use FILTER "NOSORT"
to prevent sorting by energy
bug fix: simultaneous spin/animation broken in 13.1.13
bug fix: MoldenReader fix for file blank lines and g,h,i orbitals - also
for 13.0.16
bug fix: COMPARE does not allow nSeconds at beginning, as described in
documentation
bug fix: isosurface VOLUME/AREA SET n cannot return to full array
reporting; SET -1 added.
bug fix: isosurface VOLUME/AREA always returns an array, possibly of length
0
bug fix: isosurface molecular/solvent can give inappropriate inner surfaces
bug fix: show selected includes deleted atoms
--
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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