* Download Jmol-14.15.3-binary.zip (69.8 MB)
<https://sourceforge.net/projects/jmol/files/latest/download?source=files> *
JmolVersion="14.15.3" // 2017-05-08
bug fix: SMARTS search for atropisomeric bond that is in an alicyclic ring
fails (Fred Ziegler)
- used for M/P chirality check
- for example:
load $c1cc2c3-c4c5CC2.c5ccc4C.c3(C)c1
select on smarts("a-a")
calculate chirality
print {*}.chirality.join("")
MM
bug fix: use of the less preferred name of Jmol token that has two optional
forms ("fix" vs "fixed") as a VAR does not assign that variable
name
bug fix: set cartoonRibose misses the C1'-O4' and O3'-P(+1) edges
bug fix: JVXL reader not reading Gaussian files with "1" in the third line,
5th field
bug fix: CIP M/P chirality
test: load "$2,2'-dibromobiphenyl"; calculate chirality; print
{*}.chirality.join("")
bug fix: CIP chirality nearly fully validated on ACD/Labs AY-236 set, with
some unimplemented aspects:
var skip = ({27 229}) || // E/Z only; missing chirality
({95 96 98 99 100 101 102 103 104 108 109 110 111 112 200}) ||
// trigonal planar, square planar, or hypervalent
({32 33}) || // helicene
({201 202})|| // spirocyclic central (redundant) atom
designation missing (axial designation option)
({212 213})|| // chiral conformation 1,4-benzene in a ring
({38 84}) || // ignore -- 38: Mancude for cyclopentadienyl; 84:
unknown error with P compound
({203}) || // // chiral bridgehead amine
Issue: Full implementation of the rules requires a slight modification of
Rule 1b.
Specifically, aromatic duplicate atoms must reference the sphere of their
own parent, not their
duplicated atom.
Three structures appear to be in error in the IUPAC Blue Book 2013.
,"147":"r,,,R,,,,r,,,S" // r,,,R,,,,r,,,R chiral phosphine -- I think Jmol
is right; disagrees with BB P-93.5.1.1.2 for S vs R
,"227":"SrSEErS" // S,,,,,,,r,S,,,,,,,E,,r,r // -- I think Jmol is right;
disagrees with BB P-93.5.7.2 for S vs. r
,"230":"@2D RrRsR" // r,,,R,,,,s,,,R // p 1282 -- I believe Jmol is
correct, disagrees with BB P-93.6
One structure awaiting full implementation of Rule 4b across all chirality
types, R/S, M/P, and seqCis/seqTrans
,"170":"Spp" // Jmol is missing the S -- mix of R/S and M/P for Rule 4b
- 939 lines
--
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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