Jmol.___JmolVersion="14.8.0"
Release Note: switching to semantic versioning (http://semver.org/)
Release Note: When releasing beta version, append "-beta-YYYY-MM-DD"
Release Note: new features listed are since first release of 14.5.4 (April
2016)
new feature: fully implemented CIF 2.0 reader
new feature: MagCIF reader upgraded to new IUCr standard
-- first CIF 2.0 format implemented by IUCr
-- see http://comcifs.github.io/magCIF.dic.html
new feature: x = getProperty("cifInfo", "c:/temp/test.cif")
-- reads CIF file data in structured format
-- automatically uses CIF 1.0 or CIF 2.0, as needed.
-- if file name is missing, uses current model file
new feature: 3DPrinter-compatible VRML and STL writing.
-- mesh only; does not use high-level objects Cone, Cylinder, Sphere
-- extensive use of dEF and USE for small-footprint VMRL files
-- STL is binary generally, but will be ASCII using SET DEBUG TRUE
-- write t.wrl
-- write t.stl
new feature: Jmol reads PyMOL 1.8 PSE files with "set dump_binary, 1"
new feature: load AUDIO audiofilename
-- Java and JavaScript applet can read WAV, MP3, and OGG files
-- application can read WAV files]
new feature: write CIF
-- just a very simple CIF file, P1 format
-- allows writing a simple CIF file with changed coordinates after a
UNITCELL command
new feature: full implementation of OpenSMILES and OpenSMARTS in Jmol
see http://opensmiles.org and http://www.moldb.net/opensmarts
new feature: C13 NMR prediction from
http://www.nmrdb.org/service/jsmol13c?smiles=CCCC
-- although we send MOL file, not SMILES here.
-- actuated with
SHOW NMR H1 // H1 1H H or just SHOW NMR all default to this
SHOW NMR C13 // or C or 13C
SHOW NMR none // close JSpecView
new feature: Jmol now implements a way of indicating atropisomer chirality.
-- measured dihedral angle is clockwise-positive front-to-back, as for
Jmol dihedrals
-- matching with {*}.find("SMILES","...a^nm-a...") where n and m are 1, 2,
or 3
indicate first, second, or third, respectively, and indicate which
bonds of
the biaryl bond, as written, are to the reference atoms.
-- for example:
$ load $biphenol
$ connect @{@7|@8} @{@1|@2} atropisomer
$ print {*}.find("SMARTS","c1(O)ccccc1^23-c2c(O)cccc2")
({0:13})
Explained below.
new feature: CONNECT {pair1} {pair2} ATROPISOMER
-- creates a new bond of type atropisomer (bond chirality in biaryl
systems)
-- each pair must include the bonded atom and its reference connected atom
-- example:
$ load $biphenol
$ connect @{@7|@8} @{@1|@2} atropisomer
$ getProperty bondinfo[7].type
bondinfo[7].type "atropisomer_23"
new feature: BONDORDER ATROPISOMER_nm
-- not for general use; will be found in state file
-- for example:
select BONDS ({6});
bondOrder atropisomer_23;
new feature: Jmol SMILES bond atropisomerism ^nm- and ^^nm-
-- indicates atropisomerism (bond chirality in biaryl systems)
-- ^ and ^^ for bonds similar to @ and and @@ for atoms
-- n and m are single-digit bond selectors, generally one of 1, 2, or 3
-- n = 1/2/3 means "reference atom is first/second/third bonded
-- ^- and ^^- same as ^22- and ^^22-, respectively
-- example:
$ load $biphenol
$ connect @{@7|@8} @{@1|@2} atropisomer
$ print {*}.find("SMARTS","c1(O)cccc{c1^23-c2}c(O)cccc2")
({1 6})
Here the "^23-" refers to the two carbons with connected oxygen atoms,
because the second
bond listed for the carbon on the left is to the c1(O) atom, and the
third bond listed for
the carbon on the right is to the other c(O) atom. Note that bond
numbering includes the
implicit bond to the atom coming from the atom on its left, which for the
second carbon,
starts with the atropisomeric bond itself, at least in this case.
1*23 1*23
c1(O)ccccc1^23-c2c(O)cccc2
new feature: polyhedra AUTO ...
-- sets polyhedron radius automatically, using "MAXIMUM GAP" rule
-- see Zur Abgrenzung der Koordinationssphäre und Ermittlung der
Koordinationszahl in Kristallstrukturen
G. O. Brunner, D. Schwarzenbach, Zeitschrift für Kristallographie
- Crystalline Materials, 1971, vol 133, issues 1-6 127-133
http://www.degruyter.com/view/j/zkri.1971.133.issue-1-6/zkri.1971.133.16.127/zkri.1971.133.16.127.xml?rskey=sfBNTx&result=1
new feature: polyhedron -x.x ....
-- sets maximum radius for gap calculation to be x.x
new feature: settable chain string using {atomset}.chain = "xxx"
new feature: set hiddenLinesDashed
-- when set TRUE, hidden lines in unit cells and boundbox are rendered as
dashed lines.
-- default is FALSE
new feature: $pbz1_1_.getProperty(x) where x is "info",
"faces", "faceTriangles", "faceCount",
"face_areas", "face_types", "face_points",
"vertices", ...more...
-- polyhedra information
new feature: print
unitcell("a=...,b=...,c=...,alpha=...,beta=...,gamma=....")
new feature: load ... unitcell
"a=...,b=...,c=...,alpha=...,beta=...,gamma=...."
new feature: unitcell "a=...,b=...,c=...,alpha=...,beta=...,gamma=...."
-- only the numbers are read; everything else is ignored, so order is
important here
-- uses the format created by show unitcell/a
new feature: unitcell RECIPROCAL 2
-- as integer, multiples of pi
new feature: unitcell reciprocal x.x
-- allows scaling of reciprocal cell, similar to unitcell("reciprocal",
x.x)
new feature: set echo OFFSET {sx sy sz}
-- sets the echo offset to a specific screen Angstrom offset
new feature: set echo OFFSET [mode sx sy sz ax ay az] never implemented
-- see set labelOffset
new feature: set labelOffset [mode sx sy sz ax ay az] (3.1.15, never
documented)
set labelOffset [sx, sy, sz]
set labelOffset [mode, sx, sy, sz, ax, ay, az]
where
sx,sy,sz are screen coord offsets
-- applied after view rotation
-- sy > 0 LOWERS label
ax,ay,az are xyz position (in Angstroms; applied before view rotation)
mode == 0 indicates xyz position is absolute and sx sy sz are Angstroms
mode == 1 indicates xyz position is relative to atom position and sx sy
sz are Angstroms
mode == 2 indicates xyz is absolute, and sx sy sz positions are screen
pixels
mode == 3 indicates xyz is relative, and sx sy sz positions are screen
pixels
defaults: mode == 1; ax = ay = az = 0
new feature: autocalculation of MMFF94 partial charges
-- isosurface ... map MEP
-- DIPOLE MOLECULAR
-- no need to preface these with CALCULATE PARTIALCHARGE
new feature: measure ID "test" radius 0.0 font 15.0 SansSerif Plain align
CENTER @1 @2 "test"
-- radius 0.0 turns off line (optional)
-- font... sets font (optional)
-- align [left|right|center|none] sets text alignment (optional)
-- requires ID
new feature: allowance for external app loading of binary (mmtf) files
or any other file using a simple interface:
Viewer.openReader(fullPathName, reader)
--
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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