see
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/
Jmol.___JmolVersion="14.3.16_2015.08.11"
new feature: load <mmCIF file> filter "addBonds"
-- processes _struct_conn records
-- inter-group connections only
-- includes _struct_conn bond types:
covale covalent bond
covale_base covalent modification of a nucleotide base
covale_phosphate covalent modification of a nucleotide phosphate
covale_sugar covalent modification of a nucleotide sugar
disulf disulfide bridge
metalc metal coordination
-- ignores _struct_conn bond types:
hydrog hydrogen bond
mismat mismatched base pairs
modres covalent residue modification
saltbr ionic interaction
new feature: load *1crn*
-- loads PDBe "updated" CIF files to allow CONECT-like bond creation
-- for example, http://www.ebi.ac.uk/pdbe/static/entry/1h68_updated.cif
-- suitable replacement for PDB CONECT
-- processes _chem_comp_bond and _struct_conn categories
-- presence of _chem_comp_bond will process _struct_conn as well,
regardless of filter "addbonds"
(because _chem_comp bonds are only intra-group, and for full
CONECT-like behavior, we need all bonds)
new feature: atom property "monomer" same as %g
new feature: atom property "seqcode" same as %r
new feature: load "test.pdb" from write property atomno temperature now
restores
values for atomno and temperature for points on plot
FEATURE CHANGE: javajs.awt.Dimension dependency removed from JmolViewer and
JmolStatusListener interfaces
-- changed to int[]
new feature: STEREO DTI
-- left/right dual panel, as just STEREO
-- compresses width by 50% for DTI mode (Dimension Technologies, Inc.)
new feature: set multipleBondBananas TRUE
-- displays multiple bonds as banana bonds
-- does not carry over after model loading
new feature: set multipleBondSpacing 0.15; set multipleBondRadiusFactor -1.0
-- positive number for spacing but negative for radiusFactor rotates
fixed multiple bonds 90 degrees.
new feature: [Font] button added to ScriptEditor
bug fix: a = {*}.label(...) does not work.
bug fix: "".format([a,b]) crashes Jmol
bug fix: CML reader can fail (e.g. nsc244a.cml)
bug fix: label %g does not indicate group index in chain
bug fix: JSmol does not recognize label %W %g %r %O etc. with single digits
where there is no %[xxx] equivalent
bug fix: "print stateVersion" not reporting as documented.
bug fix: write property atomno temperature "test.pdb" does not preserve
long residue names from CIF files or long atom names from other file types
bug fix: stereo setting should not be saved in state.
-- though saved, it was not by default set to normal,
-- thus influencing later loads.
bug fix: STEREO not implemented in JavaScript
bug fix: calculate STRUTS broken for 3dfr, with peptide ligand MTX
bug fix: SMARTS matching broken for [r5] ring designation
bug fix: reference to functions as commands requires lower case:
-- for example:
function F(a){ print a }
F("test") // OK
f("test") // OK
f "test" // OK
F "test" // fails
bug fix: JavaScript deletion of array elements fails for int[] arrays.
bug fix: magnetic spin vectors do not render properly (broken in
14.3.13_2015.05.12)
bug fix: config 2 and select config=2 may not work properly (still)
bug fix: minimization of PCl4 (==PC4) does not auto-switch to UFF from
MMFF94 (bond key not set)
bug fix: config 1 does not work; listing is not complete.
bug fix: format("%5.-5i") broken -- only shows right four digits if #
digits is 5.
bug fix: write PDB broken for some systems (14.3.12)
--
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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