Jmol.___JmolVersion="14.5.4_2016.04.13"
bug fix: JSmol cannot load RCSB ligand files
bug fix: "axis" unintentionally made reserved word in "14.4.4_2016.03.19"
bug fix: symop(@1 @2) broken
bug fix: symop() taking default unitcell from "current" -- should be that it
REQUIRES a prefix "{xxx}." if @1 or @2 are not indicated and there
are
multiple models (because it is a general function, not a script
command).
bug fix: models from PyMOL reader do not save atom colors in state when
balls are colored
new feature: "$isosurface1".getProperty("atoms")
-- returns atoms associated with this surface
-- for example, the atoms used to make a molecular surface
new feature: show xxx /yyy
-- filters any SHOW command for lines containing "yyy" (case insensitive)
-- examples:
$ show symop/glide
$ show set/zoom
$ show state/draw
$ show file "test.xyz" /H
$ show file "/remark 900"
$ show variables/sym
FEATURE NOTE: Jmol now has a RELATIVELY COMPLETE set of analysis and
visualization
tools for space group symmetry. All standard and magnetic space group
operations
are covered. Features are concentrated in four command options and one
function:
LOAD .... SPACEGROUP .... UNITCELL ....
SHOW SYMOP ....
DRAW SYMOP ....
DRAW POINTGROUP SPACEGROUP
x = symop(....)
With these features, you can:
-- load any model while applying any actual or conceivable space group
or subset of a space group
-- tabulate all space group operations associated with that model
-- retrieve an associative array indicating all aspects of the
operation, including
point, rotation axis, plane, glide vector, lattice offset vector, and
4x4 matrix
-- visualize all aspects of an operation, including proper and improper
rotations
inversion centers, mirror planes, glide planes, translations, and
magnetic spin time reversal
-- apply any operation to any atom or any point in space
-- given any combination of two atoms or two points in space, determine
and/or
depict the operation(s) that relate those to atoms or positions
new feature: symop(3,@3,"atom")
-- returns target atom or atoms
new feature: show symop 3 @3 "atom"
-- shows target atom or atoms
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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