Revision: 20954
http://sourceforge.net/p/jmol/code/20954
Author: hansonr
Date: 2016-02-06 18:10:59 +0000 (Sat, 06 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.5.2_2016.02.06"
new feature: isosurface BACKSHELL
-- displays just the back side of an isosurface
-- works by reversing the normals, then showing front only
-- similar to isosurface slab 50, but better if object is far from spherical
-- works with PMESH, MO, CONTACT as well
-- reverted using isosurface NOBACKSHELL
new feature: isosurface "*xxxx"
-- accesses EBI test site for ED maps at
http://wwwdev.ebi.ac.uk/pdbe/coordinates/files/%file.ccp4
-- uses default sigma 1.0
new feature: isosurface "**xxxx"
-- accesses EBI test site for ED difference maps at
http://wwwdev.ebi.ac.uk/pdbe/coordinates/files/%file_diff.ccp4
-- uses default sigma 3.0
bug fix: isosurface "==xxxx" not setting default omap cutoff and sigma 3.0
bug fix: small MRC map files mistaken for DELPHI files.
bug fix: MRC/CCP4 surface/map files still sometimes inside out.
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-06
17:04:21 UTC (rev 20953)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-06
18:10:59 UTC (rev 20954)
@@ -1174,6 +1174,7 @@
boolean isWild = (idSeen && getShapeProperty(iShape, "ID") == null);
boolean isColorSchemeTranslucent = false;
boolean isInline = false;
+ boolean isSign = false;
Object onlyOneModel = null;
String translucency = null;
String colorScheme = null;
@@ -1549,8 +1550,8 @@
case T.sign:
case T.color:
idSeen = true;
- boolean isSign = (eval.theTok == T.sign);
- if (isSign) {
+ if (eval.theTok == T.sign) {
+ isSign = true;
sbCommand.append(" sign");
addShapeProperty(propertyList, "sign", Boolean.TRUE);
} else {
@@ -2425,8 +2426,18 @@
boolean checkWithin = false;
if (filename.startsWith("*") && filename.length() > 1) {
// new PDB ccp4 option
+ if (filename.startsWith("**")) {
+ if (Float.isNaN(sigma))
+ addShapeProperty(propertyList, "sigma", Float.valueOf(sigma =
3));
+ if (!isSign) {
+ isSign = true;
+ sbCommand.append(" sign");
+ addShapeProperty(propertyList, "sign", Boolean.TRUE);
+ }
+ }
+ if (!Float.isNaN(sigma))
+ showString("using sigma=" + sigma);
filename = (String) vwr.setLoadFormat(filename, '_', false);
- // filename = info[0];
checkWithin = true;
} else if (filename.startsWith("=") && filename.length() > 1) {
checkWithin = true;
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-02-06
17:04:21 UTC (rev 20953)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-02-06
18:10:59 UTC (rev 20954)
@@ -924,7 +924,7 @@
id = id.substring(1);
String server = resolveDataBase(null, id, (isDiff ? edsUrlFormatDiff
: edsUrlFormat));
- String strCutoff = (isDiff ? "" : resolveDataBase(null, id, edsUrlCutoff));
+ String strCutoff = resolveDataBase(null, id, edsUrlCutoff);
return new String[] { server, strCutoff, isDiff ? "diff" : null };
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-06
17:04:21 UTC (rev 20953)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-06
18:10:59 UTC (rev 20954)
@@ -9,6 +9,7 @@
Jmol.___JmolVersion="14.4.2_2016.02.06"
+bug fix: isosurface "==xxxx" not setting default omap cutoff and sigma 3.0
bug fix: small MRC map files mistaken for DELPHI files, which start with the
4-byte integer 20.
bug fix: MRC/CCP4 surface/map files still sometimes inside out.
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-06 17:04:21 UTC
(rev 20953)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-02-06 18:10:59 UTC
(rev 20954)
@@ -1174,6 +1174,7 @@
boolean isWild = (idSeen && getShapeProperty(iShape, "ID") == null);
boolean isColorSchemeTranslucent = false;
boolean isInline = false;
+ boolean isSign = false;
Object onlyOneModel = null;
String translucency = null;
String colorScheme = null;
@@ -1549,8 +1550,8 @@
case T.sign:
case T.color:
idSeen = true;
- boolean isSign = (eval.theTok == T.sign);
- if (isSign) {
+ if (eval.theTok == T.sign) {
+ isSign = true;
sbCommand.append(" sign");
addShapeProperty(propertyList, "sign", Boolean.TRUE);
} else {
@@ -2425,8 +2426,18 @@
boolean checkWithin = false;
if (filename.startsWith("*") && filename.length() > 1) {
// new PDB ccp4 option
+ if (filename.startsWith("**")) {
+ if (Float.isNaN(sigma))
+ addShapeProperty(propertyList, "sigma", Float.valueOf(sigma =
3));
+ if (!isSign) {
+ isSign = true;
+ sbCommand.append(" sign");
+ addShapeProperty(propertyList, "sign", Boolean.TRUE);
+ }
+ }
+ if (!Float.isNaN(sigma))
+ showString("using sigma=" + sigma);
filename = (String) vwr.setLoadFormat(filename, '_', false);
- // filename = info[0];
checkWithin = true;
} else if (filename.startsWith("=") && filename.length() > 1) {
checkWithin = true;
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-02-06 17:04:21 UTC
(rev 20953)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-02-06 18:10:59 UTC
(rev 20954)
@@ -924,7 +924,7 @@
id = id.substring(1);
String server = resolveDataBase(null, id, (isDiff ? edsUrlFormatDiff
: edsUrlFormat));
- String strCutoff = (isDiff ? "" : resolveDataBase(null, id, edsUrlCutoff));
+ String strCutoff = resolveDataBase(null, id, edsUrlCutoff);
return new String[] { server, strCutoff, isDiff ? "diff" : null };
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-06 17:04:21 UTC
(rev 20953)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-06 18:10:59 UTC
(rev 20954)
@@ -73,6 +73,15 @@
-- works with PMESH, MO, CONTACT as well
-- reverted using isosurface NOBACKSHELL
+new feature: isosurface "*xxxx"
+ -- accesses EBI test site for ED maps at
http://wwwdev.ebi.ac.uk/pdbe/coordinates/files/%file.ccp4
+ -- uses default sigma 1.0
+
+new feature: isosurface "**xxxx"
+ -- accesses EBI test site for ED difference maps at
http://wwwdev.ebi.ac.uk/pdbe/coordinates/files/%file_diff.ccp4
+ -- uses default sigma 3.0
+
+bug fix: isosurface "==xxxx" not setting default omap cutoff and sigma 3.0
bug fix: small MRC map files mistaken for DELPHI files.
bug fix: MRC/CCP4 surface/map files still sometimes inside out.
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