Hi,
It seems the write() function now returns the result value rather than the
output from the write command. The commands:
asymunit=write("xyz")
print asymunit
should load the variable with a structure file format and give:
14
Model[1]: Jmol 14.3.14_2015.05.25 2015-05-25 23:36
C 1.92030 -0.13730 3.97996
C 0.54620 0.53560 3.97996
C -0.54620 -0.53560 3.97996
C -1.92030 0.13730 3.97996
H 2.02060 -0.75850 4.86996
H 2.02060 -0.75850 3.08996
H 2.69860 0.62590 3.97996
H 0.44590 1.15690 4.86996
H 0.44590 1.15690 3.08996
H -0.44590 -1.15690 3.08996
H -0.44590 -1.15690 4.86996
H -2.02060 0.75850 4.86996
H -2.02060 0.75850 3.08996
H -2.69860 -0.62590 3.97996
Now, instead it gives:
OK XYZ 643 c:/compchem/xyz
as if returning the result to the console and has actually written the output
to the file "xyz".
Thanks,
George
________________________________
From: Robert Hanson [hans...@stolaf.edu]
Sent: Tuesday, May 26, 2015 1:16 AM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Jmol 14.2.14/14.3.14 released
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.14/
Jmol.___JmolVersion="14.2.14_2015.05.25"
release; synchronized with 14.3.14
changes since release of 14.2.13 in March:
new feature: set contextDepthMax
-- sets the maximum depth of contexts, including {}, if{} for{} while{}
function{}
as well as the SCRIPT command and a number of expression-related situations
-- default 100
-- minimum 10
new feature: SQL "drilling" in associative arrays for sub arrays with a given
property (Rolf Huehne)
-- uses "**" as the SELECT option, sort of the way ** sometimes means
"subdirectories of"
-- returns an associative array or "" if no match
-- example:
x = [key_1:[type:"a"],key_2:[type:"b"],key_3:[type:"a"]]
z = getProperty(x, "[SELECT ** WHERE type='a']");
show z;
z = { "key_1":{ "type":"a" },"key_3":{ "type":"a" } }
new feature: for msCIF (modulated structure files), setting modulation or using
vibration ON
now also indicates occupancy changes
new feature: set showScript -1
-- turns off history (on when commands come from the keyboard)
-- stops every-second JavaScript interruptions -- Caution!
new feature: for (var i FROM [a, b]) {...}
-- same as for (var i = a; i <= b; i++) when a < b
-- same as for (var i = a; i >= b; i--) when a > b
-- much more efficient
new feature: draw polygon [@1 @2 @3...]
-- fills polygon with triangles
-- order is important -- must be cw or ccw
-- does not have to be convex
-- indeterminate result if atoms are not coplanar
-- example:
load $caffeine
draw polygon [@5 @7 @12 @13 @1 @3]
new feature: ".[a]" notation extended to x.. and allows mixing with .a.
function a(){return 1}
x = [A:[1,2,3], a:[4,5,6]]
$ print x.a.[a()]
4
$ print x..a..[a()]
4
$ print x.a..[a()]
4
$ print x..a..[a()]
4
$ print x..a.[a()]
4
$ y = x.a[1][2]; show y
y = [ 4,5 ]
new feature: "." notation extended to x.[a]
disambiguifies x[a][b][c]...
allows for variables and expressions in "." notation
i = 2
x = [1,[2 3 4 [5 6 7]],3]
show x[2].[4].[i]
==> "6"
x = [ 1,[ 2,3,4,[ 5,6,7 ],{ "testing":"now" } ],3 ]
x[i + 1].[5].["testing"] = "again"
show x
==> x = [ 1,[ 2,3,4,[ 5,6,7 ],{ "testing":"again" } ],3 ]
new feature: print command by itself clears JavaScript and Jmol consoles
new feature: color polyhedra red blue (edge color blue)
new feature: NBO command with no arguments starts NBO panel (Java application
only)
bug fix: select conformation=1 broken for non-bio CIF data
bug fix: CML reader not recognizing "fragment/join/fragment" sequence
from http://www.xml-cml.org/schema/schema3/schema.xsd (Stuart Chalk)
bug fix; 05.12 breaks Jmol.evaluate and Jmol.evaluateVar and print
getProperty("variableInfo", exp)
bug fix: using historyLevel = ... or scriptlevelMax = ... doesn't really set
these
bug fix: a number of settings have not been excluded from state scripts, which
only should save critical information for the state, not general
processing
-- no longer saved in state
-- no longer read using "set xxxxx" when that is in a state script
-- includes: historylevel;imagestate;iskiosk;useminimizationthread;
-- includes:
showkeystrokes;saveproteinstructurestate;testflag1;testflag2;testflag3;testflag4
bug fix: re-entering functions loses if/else state
bug fix: more issues with low-resolution linear-z index lines.
Need to compromise for isosurfaces and nucleic cartoons and bonds
-- which became very slow to render with precision Z placement.
bug fix: BIND can cause fault
bug fix: write "?" can cause fault when [x] box is pushed on window
bug fix: set picking dragMolecule, set picking dragMinimizeMolecule, set
picking dragLigand broken
bug fix: x = plane(@1 @2 @3) fails
bug fix: isolated bio groups such as AMP, which are not part of biopolymers,
can result in crashes
when colored or queried about their parameters (Hiroufmi Suzuki)
bug fix: new SQL ** feature needed a tweak
bug fix: set structureModifiedCallback does not work with "JmolScript:...."
bug fix: sawtooth and Legendre displacement modulations should set occupancy to
0 outside of their range.
bug fix: color atoms property vxyz crashes Jmol if no vibrations
bug fix: with msCIF, select subsystem=1 does not select anything
bug fix: vibrations in trajectories not animating (14.3.6_2014.08.14)
bug fix: reading Molden file with no MOs crashes Jmol
bug fix: color $id [30 40 50] translucent 0.8 fails
bug fix: Jmol.jar was requiring Java 1.7
bug fix: POV-Ray fixed for perspective and orthographic cameras using new
z-depth formula.
thanks: Many thanks to Laurent Proville for motivating me to look in this issue.
bug fix: perspective renderer was using the wrong formula for calculating Z
depth of pixels:
* Note added 4/2015 BH:
*
* Well, it turns out that the calculation of the intermediate pixel z value
* in all methods involving rasterization of lines is incorrect and has been
* incorrect since Jmol's inception. I noticed long ago that large triangles
such as
* produced in DRAW could incorrectly overlay/underlay other objects, but I
could
* never determine why. It turns out that the assumption that z-value is linear
* across a line when perspectiveDepth is TRUE is simply incorrect.
*
* Basically, the function z(x) is non-linear. Treating it as simply a
* linear function results in oddities where lines and planes
* -- particularly created using DRAW and large distances -- appear
* to be where they are not.
*
* Through Jmol 13.3.13 we had the standard linear relationship:
*
* z = (x - xa) / (xb - xa) * (zb - za) + za
*
* I worked it out, and, amazingly, it should be
*
* z = (xb - xa) * za * zb / ((xb - x) * zb + (x - xa) * za)
*
* Note that it is still true that when x = xb, z = zb
* and when x = xa, z = za, as required.
*
* This equation can be rearranged to
*
* z = a / (b - x)
*
* where
*
* a = (xb - xa) * za * (zb / (zb - za))
*
* and
*
* b = (xb * zb - xa * za) / (zb - za)
*
* These values must be floats, not integers, to work properly, because
* these are extrapolations from long distances in some cases. So there is
* considerable overhead there. It will take some experimentation to figure this
* out.
*
* The practical implications are for line, cylinder, and triangle drawing.
* First-pass corrections are for axes and DRAW objects. They tend to be the
* larger objects that result in the issue.
*
* Also affected is POV-Ray output, because right now POV-Ray is created using
* perspective on and plotted as though it were orthographic, but although that
* works in x and y, it does not work in z!
*
bug fix: with set dragSelected, highlight does not recognize whole molecule
bug fix: loading mmCIF data in-line loses multi-character chain IDs
bug fix: with set picking dragSelected with allowMoveAtoms FALSE and
allowRotateSelected TRUE
rotating the atoms with ALT-left ignores setting of allowMoveAtoms
// see footnotes below for ^, #, *, and $
//
// settings:^ set picking dragSelected set dragSelected
//
// move:# drag alt-shift-drag
// rotate:#* alt-drag alt-drag
// z-shift:# shift-drag (n/a)
//
// double-click:$ (starts measurement) (sets selected if set picking
SELECT)
//
// ^ set picking dragSelected overrules set dragSelected
// # all actions involve whole molecules unless set allowMoveAtoms TRUE
// * rotate requires set allowRotateSelected TRUE
// $ set dragSelected allows setting of a new molecule with double-click
when set picking SELECT
// $ set picking dragSelected allows measurements with double-click, as
usual
bug fix: for in/from broken in 14.3.13_2015.04.05
-- entering a FOR loop with empty has pops {...} context one level too far,
exiting functions
feature update: EBI validation site updated from wwwdev.ebi to www.ebi
-- for example, LOAD *1crn/val
bug fix: MO calculation hanging when G orbitals are present
bug fix: echo id myecho "testing" reports "myecho" instead of "testing"
bug fix: Molden reader broken for Dalton2015 version
bug fix: language switching not working from popup menu;
bug fix: language bundles not processed in the correct order for variants
bug fix: for (var i in hashArray) {....} broken (also in 14.2; not fixed there)
bug fix: [3 4 5].min should give integer 3, not decimal 3.0 (same with .max)
bug fix: hash values created from named int variables do not clone properly
bug fix: hash[key1]..key2.push() does not work properly
bug fix: show hash where one of the elements is an empty hash ignores that key
bug fix: local var xxx with same name of ..xxx forces lower case xxx
bug fix: local var xxx with same name of foo..xxx forces lower case xxx
bug fix: {hash}.Key = value will be stored as "key" rather than "Key" if "key"
is also a user-defined function.
bug fix: {hash}.key will fail if "key" is also a user-defined function.
bug fix: print a where a is an associative arrays fails in JavaScript (since
jmol-14.3.7_2014.08.25)
bug fix: translate SELECTED {1 1 1} @1 not working (works fine without the
SELECTED keyword)
bug fix: isosurface solvent will fail if max volume is smaller than cavity max
even though not cavity
bug fix: JmolVersion="14.3.13_2015.03.20b" broke JSmol due to error in coding
URL.js
bug fix: popup menu Symmetry broken
bug fix: PDB reader does not save unit cell on simple load
bug fix: use of {*}.xxxx = for(i;{*};....) fails
bug fix: VASP chgcar surface reader fails to recognize 10-per-line file format
bug fix: label <color ...> xxxx </color> does not calculate stringwidth
properly; set labeloffset 0 incorrect
JmolVersion="14.3.13_2015.03.13"
released
bug fix: fonts too small with antialiasDisplay (14.2.12)
bug fix: PNG generation uses iTXt instead of tEXt; problems with diacritical
marks (German translation of "March" month in creation time)
JmolVersion="14.3.13_2015.03.11"
bug fix; pdb and mmcif readers not doing biomolecule 2 properly
bug fix: load filter "bychain" broken
bug fix: x.a.push(6) does not work
bug fix: (x.a).push(3) does not work
bug fix: (x.a)[3] = 5 does not work
bug fix: show state/xxxx does not work
JmolVersion="14.3.13_2015.03.07"
synchronized with 14.2.12_2015.03.07
bug fix: x[2] = y[2] fails
--
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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