Jmol.___JmolVersion="14.14.1" // released 4/19/17
new feature: CALCULATE CHIRALITY {atom set}
-- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
-- continues with Rules 3-5, which require full-molecule analysis.
-- work in progress:
-- Rules 1 and 2 complete
-- Rule 3 (E/Z) implemented
-- Rule 4 partially implemented
-- simple linear sequences of R/S ok
-- Rule 5 not implemented
-- caveates
-- no pseudochirality
-- not cyclitols
-- does not distinguish rings, so inserts "Z" into ring bonds
-- only validated on
-- optionally limited to the given atom set (or the currently selected
atoms by default)
new feature: set jmolInJSpecView
-- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
opened in Jmol
-- default TRUE
new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
-- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
format)
-- relatively compact format
-- can speed up loading of meshes and contours
-- for filled surfaces, use .jvxl instead
-- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
-- note that binary files are NOT RECOMMENDED for JSmol because some
platforms cannot read them locally
-- example:
load $methane
isosurface plane {0 0 0 1} map vdw contours 20
write ISOSURFACE contour.pmb
isosurface contour.pmb
bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
1, 2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails
--
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
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
