Thank you, Nico, for releasing Jmol 12.3.7.
Jmol 12.3.7 fixes a few bugs and introduces two new features. Jmol can now
create a PNG file that has an extension that is basically an entire JMOL
zip file that contains all relevant files (models and meshes). In addition,
Jmol can load Z-matrix files, extending the z-matrix idea to also allow
bond order to be indicated.
bug fixes:
isosurface plane xy map ... broken
minimization broken in 12.3.6
show orientation shows incorrect zyz format if reset uses file-based
orientation matrix (smol, Sygress)
user variables should not be rest by INITIALIZE in an spt file
x3d/vrml outputting unnecessary spheres
-- bond caps within opaque atoms removed (not precisely correct to do that)
*new feature: write PNGJ
*-- creates a PNG file with appended JMOL (zip) data containing all
necessary files.
-- viewable in directories as an "icon" and readable by image readers
-- draggable back into Jmol and readable using LOAD
-- PNG file includes:
-- iTXt field "Jmol Type\0PNGJxxxxxxxxx+yyyyyyyyy"
where xxxxxxxxx is a pointer to the ZIP data
yyyyyyyyy is the number of ZIP data bytes
-- iTXt field "Software\0Jmol 12.3.7 2011-10-11 15:30"
-- iTXt field "Creation Time\0Tue, 24 Nov 2011 19:56:10 -0600"
-- yyyyyyyyy bytes of .JMOL zip data
-- show FILE "xxx.PNG" will show list of contained files, same as for a
JMOL file
-- show state FILE "xxx.PNG" will extract state, same as for a JMOL file
-- show FILE "xxx.PNG|1crn.pdb" for example will extract file, same as for
a JMOL file
*new feature: simple Z-Matrix reader
*
-- invoked by ZMATRIX:: or file starting with #ZMATRIX
-- lines starting with # are comments, which can contain jmolscript:
-- blank lines are ignored
#ZMATRIX -- methane
C
H 1 1.089000
H 1 1.089000 2 109.4710
H 1 1.089000 2 109.4710 3 120.0000
H 1 1.089000 2 109.4710 3 -120.0000
-- allows bond order specification
#ZMATRIX -- CO2
C
O 1 1.3000 2
O 1 1.3000 2 180 2
-- any position number may be replaced by a unique atom name, with number:
#ZMATRIX -- CO2
C1
O1 C1 1.3000 2
O2 C1 1.3000 O1 180 2
-- allows for dummy atoms Xn, allowing for positioning:
#ZMATRIX -- CO2
X1
X2 X1 1.0
C1 X1 1.0 X2 90
O1 C1 1.3000 X2 90 X1 0 2
O2 C1 1.3000 O1 180 X2 0 2
-- negative distance indicates that the second angle is a normal angle, not
a dihedral
#ZMATRIX -- NH3 (using simple angles only)
N1
H1 N1 1.0
H2 N1 1.0 H1 107
H3 N1 -1.0 H1 107 H2 107
-- negative distance and one negative angle reverses the chirality
#ZMATRIX -- NH3 (using simple angles only; reversed chirality)
N1
H1 N1 1.0
H2 N1 1.0 H1 107
H3 N1 -1.0 H1 -107 H2 107
-- symbolics may be used -- they may be listed first or last
#ZMATRIX
dist 1.0
angle 107
N1
H1 N1 dist
H2 N1 dist H1 angle
H3 N1 -dist H1 angle H2 angle
-- If #ZMATRIX is not the start of the file, MOPAC style is assumed.
The first two lines will be considered to be comments and ignored:
AM1
Ethane
C
C 1 r21
H 2 r32 1 a321
H 2 r32 1 a321 3 d4213
H 2 r32 1 a321 3 -d4213
H 1 r32 2 a321 3 60.
H 1 r32 2 a321 3 180.
H 1 r32 2 a321 3 d300
r21 1.5
r32 1.1
a321 109.5
d4213 120.0
d300 300.0
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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