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[Jmol-commits] SF.net SVN: jmol:[22695] trunk/Jmol
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From: <ha...@us...> - 2026-01-28 15:30:18
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Revision: 22695
http://sourceforge.net/p/jmol/code/22695
Author: hansonr
Date: 2026-01-28 15:30:13 +0000 (Wed, 28 Jan 2026)
Log Message:
-----------
Jmol.___JmolVersion="16.3.47" // (legacy) also 16.3.48 (swingJS)
bug fix: incommensurately modulated magnetic CIF file loading fails (thanks Gotzon Madariaga)
bug fix: print format("%7.5f ...", 1.0, ...) broken in 16.2.28 (thanks Gotzon Madariaga and Eric Martz)
bug fix: operation involving initial translation and both x and y loses translation
-- for example, "2/3-x-y,y,z" (thank you Dean Johnston)
bug fix: print x.format("json") fails when x is a matrix
new feature: set occupancyThreashold
-- sets the threashold for occupancy to display the atoms
-- occupancy below this value will not be displayed,
(but will still generate a halo using SELECT ON)
-- a percentage 0-100; default 50
-- particularly useful for incommensurately modulated occupation
using MODULATION ON; VIBRATION ON (thanks for idea go to Gotzon Madariaga)
new feature: matrix3x3.rxyz
-- rational xyz format extended to 3x3 matrices
-- example:
print matrix("u,-v,w").rxyz
(
1 0 0
0 -1 0
0 0 1
)
new feature: x = matrix("u,-v,w")
-- returns 3x3 matrix
-- add {0 0 0} to give 4x4
new feature: MODELKIT FILL unitcell packing
-- fills (packs) the given unit cell with atoms
-- optional packing fraction to extend packing beyond unit cell faces
-- avoids the need for LOAD "" packed or LOAD "" fill
-- does not change the space group or unit cell
-- bonding is not generated
-- only asymmetric unit atoms are required
-- unitcell can be any one of:
- Pp format "a,b,c;3/4,1/4,1/4"
- an integer lattice offset {1 0 0}, including {0 0 0}
- a non-integer lattice offset {1 0.5 0}
- a known unitcell from the file such as "unitcell_L0"
- any [origin va vb vc]
-- default unitcell is {0 0 0} (same as "a,b,c")
-- example:
load =ams/quartz 1
modelkit fill "3a,3b,c;-1,-1,0"
connect auto
new feature: spin space group split frame displays picked symop in both frames
-- with DRAW SYMOP @1 @2 or with SET PICKING SYMOP
-- example:
sdir = "https://raw.githubusercontent.com/COMCIFS/spinCIF/refs/heads/main/test/scif/"
load @{sdir + "3.6_DyCu.scif"}
modelkit fill
plot spin split
draw symop @6 @7
new feature: matrix3x3.rxyz
-- rational xyz format extended to 3x3 matrices
-- example:
print matrix("u,-v,w").rxyz
Modified Paths:
--------------
trunk/Jmol/appletweb/jsmol.zip
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/janocchio/Nmr.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
Modified: trunk/Jmol/appletweb/jsmol.zip
===================================================================
(Binary files differ)
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2026-01-28 03:36:01 UTC (rev 22694)
+++ trunk/Jmol/src/org/jmol/script/T.java 2026-01-28 15:30:13 UTC (rev 22695)
@@ -960,7 +960,7 @@
public final static int phongexponent = intparam | 28;
public final static int pickingspinrate = intparam | 29;
public final static int platformspeed = intparam | 30;
- public final static int occupancythreashold = intparam | 31;
+ public final static int occupancythreshold = intparam | 31;
public final static int propertyatomnumberfield = intparam | 32;
public final static int propertyatomnumbercolumncount = intparam | 33;
public final static int propertydatacolumncount = intparam | 34;
@@ -2695,7 +2695,7 @@
"multiProcessor",
"navigationMode",
"navigationPeriodic",
- "occupancythreashold",
+ "occupancythreshold",
"partialDots",
"pdbAddHydrogens",
"pdbGetHeader",
@@ -3782,7 +3782,7 @@
multiprocessor, // "multiProcessor"
navigationmode, // "navigationMode"
navigationperiodic, // "navigationPeriodic"
- occupancythreashold, // "occupancyThreashold"
+ occupancythreshold, // "occupancyThreshold"
partialdots, // "partialDots
pdbaddhydrogens, // "pdbAddHydrogens"
pdbgetheader, // "pdbGetHeader"
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2026-01-28 03:36:01 UTC (rev 22694)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2026-01-28 15:30:13 UTC (rev 22695)
@@ -71,7 +71,6 @@
import org.jmol.util.Parser;
import org.jmol.util.Point3fi;
import org.jmol.util.SimpleUnitCell;
-import org.jmol.util.Vibration;
import org.jmol.viewer.FileManager;
import org.jmol.viewer.JC;
import org.jmol.viewer.ShapeManager;
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2026-01-28 03:36:01 UTC (rev 22694)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2026-01-28 15:30:13 UTC (rev 22695)
@@ -340,6 +340,7 @@
setB("noDelay", noDelay);
setO("nmrPredictFormat", nmrPredictFormat);
setO("nmrUrlFormat", nmrUrlFormat);
+ setI("occupancyThreshold", occupancyThreshold);
setB("partialDots", partialDots);
setB("pdbAddHydrogens", pdbAddHydrogens); // new 12.1.51
setB("pdbGetHeader", pdbGetHeader); // new 11.5.39
@@ -559,7 +560,7 @@
//atoms and bonds
- int occupancyThreashold = 50;
+ int occupancyThreshold = 50;
boolean partialDots = false;
boolean bondModeOr = false;
boolean hbondsBackbone = false;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2026-01-28 03:36:01 UTC (rev 22694)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2026-01-28 15:30:13 UTC (rev 22695)
@@ -64,8 +64,8 @@
bug fix: print x.format("json") fails when x is a matrix
-new feature: set occupancyThreashold
- -- sets the threashold for occupancy to display the atoms
+new feature: set occupancyThreshold
+ -- sets the threshold for occupancy to display the atoms
-- occupancy below this value will not be displayed,
(but will still generate a halo using SELECT ON)
-- a percentage 0-100; default 50
Modified: trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2026-01-28 03:36:01 UTC (rev 22694)
+++ trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2026-01-28 15:30:13 UTC (rev 22695)
@@ -477,7 +477,7 @@
boolean checkOccupancy = (ms.bsModulated != null && ms.occupancies != null);
Atom[] atoms = ms.at;
int occ;
- int occMax = vwr.getInt(T.occupancythreashold);
+ int occMax = vwr.getInt(T.occupancythreshold);
boolean haveMods = false;
BS bsSlabbed = bsSlabbedInternal;
bsSlabbed.clearAll();
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2026-01-28 03:36:01 UTC (rev 22694)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2026-01-28 15:30:13 UTC (rev 22695)
@@ -5898,8 +5898,8 @@
@Override
public int getInt(int tok) {
switch (tok) {
- case T.occupancythreashold:
- return g.occupancyThreashold;
+ case T.occupancythreshold:
+ return g.occupancyThreshold;
case T.animationfps:
return am.animationFps;
case T.dotdensity:
@@ -6763,9 +6763,9 @@
public void setIntPropertyTok(String key, int tok, int value) {
switch (tok) {
- case T.occupancythreashold:
+ case T.occupancythreshold:
// 16.3.47/48
- g.occupancyThreashold = value;
+ g.occupancyThreshold = value;
break;
case T.minimizationreportsteps:
// 16.1.15 and 16.1.16
Modified: trunk/Jmol/src/org/openscience/jmol/app/janocchio/Nmr.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/janocchio/Nmr.java 2026-01-28 03:36:01 UTC (rev 22694)
+++ trunk/Jmol/src/org/openscience/jmol/app/janocchio/Nmr.java 2026-01-28 15:30:13 UTC (rev 22695)
@@ -109,7 +109,7 @@
startViewer(nmrPanel.vwr, splash, false);
- if (haveConsole)
+ if (haveJavaConsole)
nmrPanel.getJavaConsole();
nmrPanel.vwr.script("set measureAllmodels ON;font measurements 18; font labels 18;measure '2:%1.1VALUE %UNITS//hz'");
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java 2026-01-28 03:36:01 UTC (rev 22694)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java 2026-01-28 15:30:13 UTC (rev 22695)
@@ -531,7 +531,7 @@
}
public void getJavaConsole() {
- if (!jmolApp.haveConsole || !allowJavaConsole)
+ if (!jmolApp.haveJavaConsole || !allowJavaConsole)
return;
// Adding console frame to grab System.out & System.err
consoleframe = new JFrame(GT.$("Jmol Java Console"));
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