Jmol users,
Well, January is about over. St. Olaf has an "interim" - a one-month period
where a single course is taken. Every few years I get this period off, and
this was one. I focused on Jmol and in particular three aspects:
crystallography, rapid prototyping, and multi-touch. I'm happy to report
that we have significant advances in those areas. The bad news is that the
list below needs to get documented, and I have no idea when I'll get to it.
So this list must serve for now as a guide to what's new in Jmol.
Time for a break, I think...
The list is organized into 16 categories:
NEW SHAPE: STRUTS
NEW COMMAND: LOG
SELECT
MEASURE
CALCULATE
PICKING
SPACEFILL
BOUNDBOX
ZOOM
DRAW
SYMMETRY
SURFACES
FILE LOADING
MULTITOUCH
MEMORY
MISCELLANEOUS
The latest version is now available at the usual location:
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Bob
SUMMARY -- new features, Jmol versions 11.9.11-23 (Dec 2009/Jan 2010)
NEW SHAPE: STRUTS
-----------------
# new feature: for the Center for Biomolecular Modeling, Milwaukee School of
Engineering
# contributed ideas of Mark Hoeltzer for rapid prototyping.
# new feature: STRUTS shape -- for rapid prototyping -- these are sticks
that
# can be connected anywhere but are not measures and are not
covalent bonds
# new feature: calculate STRUTS -- contributed algorithm of George Phillips
# ([email protected]) automates introduction of struts
# new feature: set strutSpacing 6 -- George's "DELTA"
# new feature: set strutLengthMaximum 7.0 -- George's "THRESH"
# new feature: set strutDefaultRadius 0.3 -- default rendering (will be
translucent white as well)
# new feature: set strutsMultiple (default FALSE) allows multiple struts on
a given atom
NEW COMMAND: LOG
----------------
# new feature: set LOGFILE "name" -- log file will be "JmolLog_" + name
# in the Jar file directory -- note that this is not
# ever possible with the web-based version, even with the
# signed applet, but signed applet or application running
# locally can write to this file
#
# set logFile "test"
# new feature: LOG command -- same as print but to the log file
# can be prepended with nicely formatted date with "NOW" as the
# first three characters
#
# log "NOW\n" + getProperty("modelInfo")
#
SELECT
------
# new feature: select configuration=1 same as "configuration 1", but with no
shape updating
MEASURE
-------
# new feature: math function measure({exp1},{exp}[,{exp}[,{exp}]],min, max,
format, units, "CONNECTED")
# all optional after the first two expressions (or coordinates)
# min/max in Angstroms
# format of the sort "%a1 %a2 %5.3VALUE %UNITS"
# units may be "pm", "nm", "au", or "angstroms"(default/unknown)
# "CONNECTED" indicates that the atoms must be connected as well
# for example:
#
# print measure({carbon}, {oxygen}, 1.2, 1.5,
"%a1%i1\t%a2%i2\t%3.0VALUE\t%UNITS", "pm", "CONNECTED")
# new feature: measure ticks {major,minor,subminor} format ["%0.2f", ...]
scale {x y z}|x.xx first x.xxx {point1} {point2}
CALCULATE
---------
# new feature: calculate hydrogens (including formal charge)
# new feature: minimize ADDHYDROGENS # minimizes and then adds hydrogen
# new feature: calculate hydrogens (including formal charge)
PICKING
-------
# new feature: set picking CONNECT -- like measuring distances, except you
get bonds.
# new feature: set picking DELETEBONDS -- opposite idea -- click two atoms
generally,
# or, with set BONDPICKING, click
the center of the bond
# new feature: set picking STRUTS
SPACEFILL
---------
# new feature: spacefill AUTO
# new feature: spacefill JMOL
# new feature: spacefill BABEL
# new feature: spacefill BABEL21
# new feature: spacefill RASMOL
# new feature: spacefill 20%JMOL
# new feature: spacefill 23%BABEL
# etc.
#
# default atom size changed from 20%Jmol to 23%Auto for C atom size match in
small molecules
# new feature: update of Babel VDW forces. We had been using Babel 1.0
numbers
# that were changed long ago;
# new feature: set defaultVDW BABEL21 -- older 2.1 numbers previously
"BABEL"
# bug fix: MAJOR -- proper model-based Van der Waals radii.
# this bug has been with Jmol since its inception -- that
# the inflated Jmol parameters for H, C, N, and O are not
# proper for anything but traditional "no hydrogen" PDB files
# That "Jmol" data set should not be used with small molecules,
# and it has long been noted that it looks incorrect. While we
# have had the (old) Babel data set, one should not have to
# know to use that manually. The new feature associated with this
# fix is
#
# set defaultVDW AUTO (default)
#
# So now Jmol will apply a proper Babel-based VDW set when
# the file has hydrogen atoms present. One can always override this
# if desired, but I think the only reason to do that is to have
# the identical match to an improperly defined VDW size in previous
# output.
#
# Note -- script files already in place will not be affected,
# as they explicitly define defaultVDW to be JMOL.
AXES/BOUNDBOX/UNITCELL
----------------------
# new feature: axes labels "x" "y" "z"
# new feature: axes labels ON
# new feature: axes labels OFF
# new feature: axes ticks [x|y|z] {major,minor,subminor} format ["%0.2f",
...] scale {x y z}|x.xx (state fixed)
# new feature: boundbox $isosurface1
# new feature: boundbox SCALE x.x option:
# boundbox scale 0.5 # scales the current boundbox
# boundbox scale 1.1 {*} # scales the boundbox to 10% larger than usual
# boundbox scale 1.1 CORNERS {first} {second}
# boundbox scale 1.1 {center} {cornerVector}
# boundbox scale 1.1 $isosurface1
# new feature: boundbox ticks [x|y|z] {major,minor,subminor} format
["%0.2f", ...] scale {x y z}|x.xx first x.xxx
# new feature: unitcell ticks ..... with special option "scale hkl" to
indicate unit cell dimension scaling
ZOOM
----
# new feature: zoom in; zoomTo in
# new feature: zoom out
DRAW
----
# new feature: draw POLYGON
# really for the state after definition of an intersection
# but also useable in principal:
#
# draw POLYGON nVertices {vert1} {ver2} ...
# nFaces [face1] [face2] [face3]
#
# where [face1] is a triangle definition (not quadralateral)
# consisting of either three integers: [v1 v2 v3]
# or four integers: [v1 v2 v3 meshCode]
#
# v1,v2,v3 point to vertices (0-based)
# meshCode is a bitset number 0-7 indicating which edges of the
# polygon are to be displayed in "mesh" format:
#
# 0 no edges
# 1 v1-v2 edge
# 2 v2-v3 edge
# 4 v3-v1 edge
# 3,5,6,7 -- combinations of the above three
#
# if meshCode is not included, it is registered as 7 (all edges)
#
# This be useful for objects that have very sharp edges, like cubes.
#
# new feature: draw BOUNDBOX (backlit for backside only)
# new feature: draw UNITCELL (backlit for backside only)
# these both allow for scaling:
# draw scale 2.0 UNITCELL MESH NOFILL
# draw scale 0.8 BOUNDBOX POINTS NOFILL
# new feature: draw INTERSECTION BOUNDBOX HKL {h k l}
# new feature: draw INTERSECTION UNITCELL HKL {h k l}
# new feature: draw INTERSECTION BOUNDBOX PLANE {a b c d}
# new feature: draw INTERSECTION UNITCELL PLANE {a b c d}
SYMMETRY
--------
# new feature: draw SYMOP {atom1} {atom2}
# new feature: draw SYMOP n {atom1} {atom2}
# extends draw SYMOP n {atom}
# extends draw SYMOP n
# new feature: show SYMOP {atom1} {atom2}
# new feature: show SYMOP n {atom1} {atom2}
# new feature: show SYMOP n
# new feature: show SYMOP
# new feature: math function hkl(a,b,c)
SURFACES
--------
# new feature: XPLOR/CNS electron density reader
# new feature: CCP4/MRC electron density reader
# new feature: isosurface INLINE @x
# new feature: isosurface SLAB {plane definition} [optional offset]
# new feature: colorscheme TRANSLUCENT [color scheme name]
# goes from transparent to opaque across any color
scheme
# new feature: colorschemes BW and WB (Black/white, white/black)
# new feature: isosurface COLOR DENSITY option produces a point-graph of
grid colored by
# grid point value rather than an isosurface
# new feature: cloud rendering of electron density using
#
# isosurface color DENSITY cutoff 0
#
# and typically some "traslucent" colorscheme such as translucent bw:
#
# isosurface color density cutoff 0 boundbox colorscheme translucent
bw \
# color range 1.0 3.0 within 2.0 {*} "3hyd_map.ccp4" mesh
nofill
# new feature: isosurface OFFSET {x, y, z}
# new feature: isosurface SCALE3D x.xx Creates a "mountain" plot from a
planar map
# new feature: isosurface CENTER option for CCP4,MRC,XPLOR files
# allows centering offsets in crystallographic grid coordinates
of map file
# new feature: anisotropy {scaleX scaleY scaleZ} and center now implemented
# for all file-based and function-based isosurfaces.
# scales are factors data coordinates are to be multiplied
# by for display in the Jmol coordinate system. So, for
example,
#
# pmesh ANISOTROPY {0.1 1 1} center {-4 0 0} "pmesh.bin"
#
# compresses the surface along x and causes data {0 0 0} to
appear
# at Jmol coordinate {-4 0 0}
# new feature: isosurface within 2.0 {points}
# gives true calculation of surface within that distance
# of ANY atom in the set, not just the center
# (isosurface WITHIN was introduced in Jmol 11.1.21 but not documented
# new feature: getproperty "shapeInfo.isosurface[1].xyzMin"
# new feature: getproperty "shapeInfo.isosurface[1].xyzMax"
# new feature: getproperty "shapeInfo.pmesh[1].xyzMin"
# new feature: getproperty "shapeInfo.pmesh[1].xyzMax"
# new feature: ALL JVXL OUTPUT TO XJVXL validated XML FORMAT
# new feature: XJVXL excludedVertexData and excludedTriangleData
# for particularly accurate rendering of isosurfaces
# new feature: write PMESH creates XJVXL file
# new feature: write MESH t.mesh JVXL "vertex-only" very compact style mesh
surface
# new feature: JVXL files for molecular orbitals readable as CML, including
atom positions
FILE LOADING
------------
# new feature: VASP vasprun.xml reader http://cms.mpi.univie.ac.at/vasp/
# new feature: AMPAC reader
# new feature: load/isosurface "filename" AS "myfile" loads the file
# and saves it as file "myfile"
# thus accomplishing an optional local file caching system.
# also saves the LOCAL version in the state.
# new feature: xyz files with 9th column is atom number
# new feature: embedded scripts in PovRay, JPG, and PNG files stripped of
local file path,
# so will run from any directory having that file also in it.
# new feature: DGRID reader (
http://cqb.fc.ul.pt/intheochem/nuno/data/dgrid-4.4.zip)
#
http://www.scm.com/Doc/Doc2009.01/ADF/ADFUsersGuide/page430.html
# new feature: ADF orbital reading -- MOs go into LAST model frame
MULTITOUCH
----------
# new feature: -Msparshui, -Msparshui-simulated for application
# multiTouchSparshUI=true or multiTouchSparshUI-simulated=true
for applet
# requires prior starting of JmolMultiTouchDriver.exe,
currently set up
# only for HP TouchSmart computer.
# Uses a modified SparshUI interface over port 5946 (client)
and 5947 (device).
# Multi-touch gestures include a two-finger drag to translate
and a two-finger
# spread/pinch to zoom in/out.
# In addition, a one-finger flick starts spinning.
MEMORY
------
# new feature: set preserveState FALSE (default TRUE) --
# for some applications it can be helpful to turn off the
# feature of preserving the state in order to save memory
# * This flag if set FALSE:
# *
# * 1) turns UNDO off for the application
# * 2) turns history off
# * 3) prevents saving of inlinedata for later LOAD "" commands
# * 4) turns off the saving of changed atom properties
# * 5) does not guarantee accurate state representation
# *
# * It is useful in situations such as web sites where
# * memory is an issue and there is no need for such.
# *
# *
MISCELLANEOUS
-------------
# new feature: -{plane definition} refers to opposite-facing plane as {plane
definition}
# new feature: PDB trajectory for concatenated PDB files (no "MODEL" line)
# new feature: show state [name]
# new feature: all saved orientations now saved in state
# new feature: at the console, set xx[tab] completes xx with all matching
set parameters
# (and load "xxx[tab] completes the file name with available
choices)
# new feature: set SLABBYATOM no partial atoms or bonds
# new feature: set SLABBYMOLECULE no partial molecules
# new feature: set zshadePower -- log_2(p) in f = [(zDepth - z) / (zDepth
- zSlab)]^p
# new feature: set phongExponent like set specularExponent, but se = 2^pe
# new feature: optional set saveProteinStructureState usually TRUE
# but can be set to FALSE to not write helix/sheet/turn data to
state
# new feature: color fractions as points: {0.5, 0.5, 1} or [0.5 0.5 1]
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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