Revision: 20126
http://sourceforge.net/p/jmol/code/20126
Author: hansonr
Date: 2014-11-25 12:43:48 +0000 (Tue, 25 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.9_2014.11.24"
bug fix: reading of JVXL file saved with noFill still does fill
bug fix: CASTEP DENSITY surface file reader does not do downsampling
new feature: isosurface "==1blu"
-- difference map fo-fc
-- defaults to sigma=3
-- automatically implements SIGN option
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
2014-11-25 12:42:40 UTC (rev 20125)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
2014-11-25 12:43:48 UTC (rev 20126)
@@ -109,16 +109,16 @@
rd();
}
} else {
- for (int i = 0; i < nFilePoints; i++) {
- int x = parseIntStr(line) - 1;
- int y = parseInt() - 1;
- int z = parseInt() - 1;
- if (nSkip > 0)
- skipPoints(nSkip);
- voxelData[x][y][z] = recordData(parseFloat());
- rd();
+ for (int i = 0; i < nFilePoints; i++) {
+ int x = parseIntStr(line) - 1;
+ int y = parseInt() - 1;
+ int z = parseInt() - 1;
+ if (nSkip > 0)
+ skipPoints(nSkip);
+ voxelData[x][y][z] = recordData(parseFloat());
+ rd();
+ }
}
- }
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-25 12:42:40 UTC
(rev 20125)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-25 12:43:48 UTC
(rev 20126)
@@ -4147,8 +4147,11 @@
Logger.error(key + " -- could not read " + strCutoff);
}
if (cutoff > 0) {
- if (diff != null && Float.isNaN(sigma))
- sigma = 3;
+ if (diff != null) {
+ if (Float.isNaN(sigma))
+ sigma = 3;
+ addShapeProperty(propertyList, "sign", Boolean.TRUE);
+ }
showString("using cutoff = " + cutoff + (Float.isNaN(sigma) ? ""
: " sigma=" + sigma));
if (!Float.isNaN(sigma)) {
cutoff *= sigma;
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2014-11-25
12:42:40 UTC (rev 20125)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2014-11-25
12:43:48 UTC (rev 20126)
@@ -1462,11 +1462,9 @@
@Override
public void notifySurfaceMappingCompleted() {
- if (!thisMesh.isMerged) {
- thisMesh.initialize(sg.isFullyLit() ? T.fullylit
- : T.frontlit, null, sg.getPlane());
- thisMesh.setJvxlDataRendering();
- }
+ if (!thisMesh.isMerged)
+ thisMesh.initialize(sg.isFullyLit() ? T.fullylit : T.frontlit, null,
+ sg.getPlane());
setBsVdw();
thisMesh.isColorSolid = false;
thisMesh.colorDensity = jvxlData.colorDensity;
@@ -1477,8 +1475,13 @@
explicitContours = true;
if (explicitContours && thisMesh.jvxlData.jvxlPlane != null)
thisMesh.havePlanarContours = true;
- setPropertySuper("token", Integer.valueOf(explicitContours ? T.nofill :
T.fill), null);
- setPropertySuper("token", Integer.valueOf(explicitContours ?
T.contourlines : T.nocontourlines), null);
+ setPropertySuper("token",
+ Integer.valueOf(explicitContours ? T.nofill : T.fill), null);
+ setPropertySuper("token",
+ Integer.valueOf(explicitContours ? T.contourlines : T.nocontourlines),
+ null);
+ if (!thisMesh.isMerged)
+ thisMesh.setJvxlDataRendering();
Lst<Object[]> slabInfo = sg.getSlabInfo();
if (slabInfo != null) {
thisMesh.slabPolygonsList(slabInfo, false);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-25 12:42:40 UTC
(rev 20125)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-25 12:43:48 UTC
(rev 20126)
@@ -17,9 +17,13 @@
Jmol.___JmolVersion="14.3.9_2014.11.24"
+bug fix: reading of JVXL file saved with noFill still does fill
bug fix: CASTEP DENSITY surface file reader does not do downsampling
-new feature: isosurface "==1blu" -- difference map; defaults to sigma=3
+new feature: isosurface "==1blu"
+ -- difference map fo-fc
+ -- defaults to sigma=3
+ -- automatically implements SIGN option
JmolVersion="14.3.9_2014.11.23"
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