Jmol Users,
This release will be followed in a week with a synchronized Jmol 14.0.8.
Testing this week much appreciated!.
Executive summary:
Jmol 14.1.8 adds several new features requested by users, including
- a new setting that displays ribose rings in cartoons (Rick Spinney)
- a simplified format for display of sequences of frames in forward and
reverse direction, especially for IRC sequences (Henry Rzepa)
- updated Tinker file reader (also Folding@Home; George Whitwell)
- the ability to get correlated lists of atoms between two models of the
same compound from two different sources or one 2D and one 3D
(used in JSpecView/Jmol/JSME integration)
- full explicit-hydrogen SMILES generation option
Bug fixes include some new and some very old but only recently discovered
bugs in a variety of areas. Many thanks for those who reported these.
Some stats from the tracker installed in late December that tracks actual
page visits by end users of Jmol of participating pages:
For the period Jan 6 - Feb 5, 2014:
Visits 105,175
Unique Visitors 74,425
Pageviews 238,037
Pages / Visit 2.26
Avg. Visit Duration 00:04:23
Bounce Rate 64.14%
% New Visits 69.02%
Interesting!
--Bob Hanson
___JmolVersion="14.1.8"
JmolVersion="14.1.8_dev_2014.02.06"
new feature: set cartoonRibose
-- draws in ribose rings, with facets showing puckering
-- connects via C4'-C5'-O5'-P explicitly
-- shows C3'-O3' for reference.
-- disables cartoonBaseEdges (Leontis-Westhof Edges)
-- disabled by SET cartoonBaseEdges ON
-- suggested by Rick Spinney, Ohio State
new feature: anim frame [a,b,c,d] works with negative numbers to indicate
ranges:
-- anim frame [1, -5, 10, -6] --> [1,2,3,4,5,10,9,8,7,6]
-- read as "1 through 5 and then 10 through 6"
new feature: Tinker file reader (and FoldingXYZ reader upgrade)
-- Can use Tinker:: but this is only required if first line is JUST an
atomCount
-- accommodates older Tinker format with n-1 atoms for atomCount
-- allows for trajectories and desired model number
new feature: (actually 13.1 but undocumented) animation frame [ 51 50 49 48
47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....]
new feature: x = compare({atomset1}, {atomset2}, "MAP")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "all")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "best")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "H")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "allH")
new feature: x = compare({atomset1}, {atomset2}, "MAP", "bestH")
-- generates one or more correlations lists based on non-aromatic SMILES
-- optionally includes H atoms
-- optionally generates all possible atom mappings
-- returns int[][] = [ [a1 b1],[a2 b2],[a3 b3],... ]
where an and bn are integer atom indices
or list<int[][]> when "all" option is chosen.
-- the following will generate one atom correlation
map for two structures including hydrogen atoms:
load files "a.mol" "b.mol"
x = compare({1.1} {2.1} "MAP" "H")
(useful for 2D/3D model atom matching)
-- the following compares the model of caffeine from NCI to that from
PubChem:
load $caffeine;load append :caffeine;frame *
select 2.1; label %[atomIndex]
compare {1.1} {2.1} SMILES rotate translate
x = compare({1.1}, {2.1}, "MAP" "bestH")
for (a in x) {a1 = a[1];a2=a[2];select atomindex=a1;label @a2}
new feature: compare {model1} {model2} SMILES
-- no need to give SMILES; Jmol can generate it from {model1}
new feature: x = {*}.find("SMILES", "H")
-- generates SMILES with explicit H atoms
bug fix: substructure() function using SMILES instead of SMARTS, so only
full structures;
bug fix: better error trapping and messages in SMILES-related methods
bug fix: make webexport discovery of path to Jmol.jar and jsmol.zip more
robust.
bug fix: getProperty extractModel not honoring subset
bug fix: set pdbGetHeader TRUE does not capture REMARK3 REMARK290 REMARK350
bug fix: getProperty("JSON",....) should wrap value in {value:...}
bug fix: MO persistent translucency broken in 11.x
bug fix: show MENU write MENU load MENU all broken in 12.2
bug fix: {*}[n] should be empty if nAtoms <=n
bug fix: abinit reader was nonfunctional
bug fix: assign atom into into PDB file loses atom names
bug fix: y = ([3])[1][1] should be [3] not 3
bug fix: break n nonfunctional
bug fix: format() and label() functions limited to 4 arguments; should be
unlimited
bug fix: errors in paths to js code in web export templates.
--
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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