Jmol users -- some new functionality and some bug fixes
version=11.5.38 (soon to be released)
# bug fix: select n-m:c chain selection inappropriately case sensitive
When the group range business was extended to allow non-existent start
and end points, a bug was introduced that forced case-sensitive chain
designations even without set chainCaseSensitive TRUE.
other fixes:
# bug fix: draw CIRCLE for multiple models
# bug fix: zap of quaternion also zaps model inappropriately
# bug fix: zap to one model assigns -1 to currentModelIndex instead of 0
# bug fix: application -- "make crystal..." menu item does nothing --
removed
A remnant of Jmol 9 that was never removed? I don't know the history of
this; only that it doesn't exist in Jmol 10 or 11.
new features:
# new feature: set drawPicking now enables measuring among atoms and
DRAW points
# -- not saved -- just transient measurements
THIS IS GOOD - you can now double-click on those points and lines you
create using DRAW and see a measurement of distance or angle to other
points or atoms. For this you need to specify SET DRAWPICKING TRUE. You
can't "lock" these measurements in (yet).
# new feature: random(a), a random number between 0 and a
# new feature: random(a,b) a random number between a and b
# new feature: set pdbSequential (default FALSE) for custom PDB files
# -- bypasses inter-group bonding check when creating polymers
This flag can be used if the PDB data are something other than standard
PDB files.
# new feature: draw CIRCLE [FILL | MESH NOFILL] more intuitive
open/filling syntax
The default for CIRCLE is now same as plane -- filled. Use "MESH NOFILL"
to draw a ring.
# new feature: draw VECTOR {atom center} {dx dy dz}
Allows definition of a simple arrow from an origin along a specified
direction. Can be scaled using the SCALE option.
# new feature: draw with mixed types processes them in order
# (11.4 does {x,y,z}, then $xxx, then {atomExpression}, then
@{{atoms}.split()})
OK, this is a change -- prior to this you couldn't mix atoms and
coordinates in any reasonable way. All coordinates were grouped first,
then all $xxx points, then all atom expressions.
# new feature: draw .... ">xxx" first character of title ">" forces
title to
# last point, not first
Just to allow some flexibility with title placement.
# new feature: set quaternionFrame "c" "p" "q"
# - "c" -- CA-C and CA-N, as per Andy Hanson
# - "q" -- peptide plane CA-C and N'-CA' as per J.R.Quine
# - "p" -- peptide plane CA-C and C-N'
# new feature: write QUATERNION S -- creates vector script
Ask me if you are interested in quaternions.
Bob
--
Robert M. Hanson
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
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
