Am 11.05.2011 19:08, schrieb Robert Hanson:
2011/5/11 Reinhold Störmann <[email protected]
<mailto:[email protected]>>
But I still get some strange behavior of the jmol Applet that
doesn't necessarily have to be caused by my script:
After opening the jmol menue (right mouse button), a small warning
symbol appears to the right of the first menu entry ("all
molecules") and subsequently the menu doesn not open again on
klicking the right mouse button.
(jmol 12.0.39, java 1.6.0_25, Vista, FF 4.0 or Opera 10)
That would be a Java bug. I've worked with them before on this, and we
settled on the nuanced warning rather than a big bright frame or
something worse. Sounds like there may be an issue there. Lately I
haven't seen it, but that does sound like a problem. If you can report
back what is in the Java console (Java, not Jmol) after that, it would
be good to see. I doubt there is anything there, though. I'm using
1.6.0_24.
Any idea, why I can't open the menu again (e.g. to select another
molecule to rotate)?
Is something syntactically wrong in the commands?
Try opening the menu by clicking on the Jmol logo in the bottom right
corner.
Reinhold
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--
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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I tried your suggested work-around for the supposed java bug to open the
jmol menu by clicking on the jmol logo. That works.
Also the java console does not give any hint about the bug that's
causing the problem.
Java Plug-in 1.6.0_25
Verwendung der JRE-Version 1.6.0_25-b06 Java HotSpot(TM) Client VM
Home-Verzeichnis des Benutzers = C:\Users\cheops
----------------------------------------------------
c: Konsole löschen
f: Objekte in Finalisierungswarteschlange finalisieren
g: Speicherbereinigung
h: Diese Hilfemeldung anzeigen
l: ClassLoader-Liste ausgeben
m: Speicherbelegung anzeigen
o: Protokollierung auslösen
q: Konsole ausblenden
r: Richtlinien-Konfiguration neu laden
s: System- und Bereitstellungseigenschaften ausgeben
t: Threadliste ausgeben
v: Thread-Stack ausgeben
x: ClassLoader-Cache löschen
0-5: Trace-Stufe auf <n> setzen
----------------------------------------------------
The text above is the only thing in java console. There is a second java
console open, but that contains jmol commands and messages:
Java Plug-in 1.6.0_25
Verwendung der JRE-Version 1.6.0_25-b06 Java HotSpot(TM) Client VM
Home-Verzeichnis des Benutzers = C:\Users\cheops
----------------------------------------------------
c: Konsole löschen
f: Objekte in Finalisierungswarteschlange finalisieren
g: Speicherbereinigung
h: Diese Hilfemeldung anzeigen
l: ClassLoader-Liste ausgeben
m: Speicherbelegung anzeigen
o: Protokollierung auslösen
q: Konsole ausblenden
r: Richtlinien-Konfiguration neu laden
s: System- und Bereitstellungseigenschaften ausgeben
t: Threadliste ausgeben
v: Thread-Stack ausgeben
x: ClassLoader-Cache löschen
0-5: Trace-Stufe auf <n> setzen
----------------------------------------------------
urlImage=jar:http://localhost/local/fernandez/external/jmol/JmolApplet0.jar!/jmol75x29x8.gif
Jmol applet jmolAppletcation__999342465799502__ initializing
AppletRegistry.checkIn(jmolAppletcation__999342465799502__)
1714 script command tokens
applet context: -applet
appletDocumentBase=http://localhost/local/fernandez/showmodel.php?model1=NF-270&model2=IM14&model3=%28CF3SO2%292N&wwidth=800&wheight=600
appletCodeBase=http://localhost/local/fernandez/external/jmol/
(C) 2009 Jmol Development
Jmol Version: 12.0.39 2011-02-04 07:47
java.vendor: Sun Microsystems Inc.
java.version: 1.6.0_25
os.name: Windows Vista
memory: 4.6/16.3
processors available: 2
useCommandThread: false
appletId:jmolAppletcation__999342465799502__
defaults = "Jmol"
backgroundColor = "#000000"
language=de
FileManager.getAtomSetCollectionFromFile(models/NF-270.pdb)
FileManager opening http://localhost/local/fernandez/models/NF-270.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/NF-270.pdb): 1008 ms
reading 186 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty
"auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
ambientPercent = 45
showMultipleBonds = false
allowRotateSelected = true
dragSelected = true
FileManager.getAtomSetCollectionFromFile(models/IM14.pdb)
FileManager opening http://localhost/local/fernandez/models/IM14.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/IM14.pdb): 58 ms
reading 25 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 models in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
2 models
FileManager.getAtomSetCollectionFromFile(models/(CF3SO2)2N.pdb)
FileManager opening http://localhost/local/fernandez/models/(CF3SO2)2N.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/(CF3SO2)2N.pdb): 38 ms
reading 15 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 models in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
Default Van der Waals type for model set to Jmol
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
3 models
setStatusAtomPicked(207,[LLL]0:A.C/2.1 #22 -5.3395004 0.2278 -0.0025)
setStatusAtomPicked(216,[LLS]445:A.F/3.1 #6 9.400803 13.966837 -7.14811)
setStatusAtomPicked(215,[AZD]1408:A.O/3.1 #5 11.119125 11.45979
-7.0131083)
setStatusAtomPicked(16,[LCL]404:A.C/1.1 #17 9.181296 4.3736672 -1.5907942)
setStatusAtomPicked(190,[KCD]469:A.N/2.1 #5 -0.425 1.3298999 -1.0E-4)
setStatusAtomPicked(17,[LCL]404:A.C/1.1 #18 8.779366 3.1873903 -0.9474809)
setStatusAtomPicked(214,[AZD]1408:A.O/3.1 #4 5.844434 7.811645 6.2802634)
setStatusAtomPicked(44,[LLW]0:A.C/1.1 #45 9.823229 -0.27577254 1.0702245)
Jmol applet jmolAppletcation__844061985409492__ initializing
AppletRegistry.checkIn(jmolAppletcation__844061985409492__)
applet context: -applet
appletDocumentBase=http://localhost/local/fernandez/showmodel.php?model1=NF-270&model2=IM14&model3=%28CF3SO2%292N&wwidth=800&wheight=600
appletCodeBase=http://localhost/local/fernandez/external/jmol/
(C) 2009 Jmol Development
Jmol Version: 12.0.39 2011-02-04 07:47
java.vendor: Sun Microsystems Inc.
java.version: 1.6.0_25
os.name: Windows Vista
memory: 16.1/26.3
processors available: 2
useCommandThread: false
appletId:jmolAppletcation__844061985409492__
urlImage=jar:http://localhost/local/fernandez/external/jmol/JmolApplet0.jar!/jmol75x29x8.gif
defaults = "Jmol"
backgroundColor = "#000000"
language=de
FileManager.getAtomSetCollectionFromFile(models/NF-270.pdb)
FileManager opening http://localhost/local/fernandez/models/NF-270.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/NF-270.pdb): 132 ms
reading 186 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty
"auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
ambientPercent = 45
showMultipleBonds = false
allowRotateSelected = true
dragSelected = true
FileManager.getAtomSetCollectionFromFile(models/IM14.pdb)
FileManager opening http://localhost/local/fernandez/models/IM14.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/IM14.pdb): 6 ms
reading 25 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 models in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
2 models
FileManager.getAtomSetCollectionFromFile(models/(CF3SO2)2N.pdb)
FileManager opening http://localhost/local/fernandez/models/(CF3SO2)2N.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/(CF3SO2)2N.pdb): 3 ms
reading 15 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 models in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
Default Van der Waals type for model set to Jmol
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
3 models
Jmol applet jmolAppletcation__844061985409492__ destroyed
Jmol applet jmolAppletcation__6393371223002793__ initializing
AppletRegistry.checkIn(jmolAppletcation__6393371223002793__)
applet context: -applet
appletDocumentBase=http://localhost/local/fernandez/showmodel.php?model1=NF-270&model2=IM14&model3=%28CF3SO2%292N&wwidth=800&wheight=600
appletCodeBase=http://localhost/local/fernandez/external/jmol/
(C) 2009 Jmol Development
Jmol Version: 12.0.39 2011-02-04 07:47
java.vendor: Sun Microsystems Inc.
java.version: 1.6.0_25
os.name: Windows Vista
memory: 15.4/36.3
processors available: 2
useCommandThread: false
appletId:jmolAppletcation__6393371223002793__
urlImage=jar:http://localhost/local/fernandez/external/jmol/JmolApplet0.jar!/jmol75x29x8.gif
defaults = "Jmol"
backgroundColor = "#000000"
language=de
FileManager.getAtomSetCollectionFromFile(models/NF-270.pdb)
FileManager opening http://localhost/local/fernandez/models/NF-270.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/NF-270.pdb): 39 ms
reading 186 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty
"auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
ambientPercent = 45
showMultipleBonds = false
allowRotateSelected = true
dragSelected = true
FileManager.getAtomSetCollectionFromFile(models/IM14.pdb)
FileManager opening http://localhost/local/fernandez/models/IM14.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/IM14.pdb): 5 ms
reading 25 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 models in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
2 models
FileManager.getAtomSetCollectionFromFile(models/(CF3SO2)2N.pdb)
FileManager opening http://localhost/local/fernandez/models/(CF3SO2)2N.pdb
The Resolver thinks Pdb
Setting space group name to P 1
openFile(models/(CF3SO2)2N.pdb): 3 ms
reading 15 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 models in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
Default Van der Waals type for model set to Jmol
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
3 models
So, how can we find out what causes the problem? If java is the culprit,
should I downgrade to 1.6.0_24 or upgrade to 1.6.0_26?
On the jmol side:
I get unexpected behavior when selecting one molecule of the three
displayed by using the "set picking - select molecule" command from the
jmol menu. It seems that not the molecule I click on is selected, but
the two molecules I did not click on are selected (ALT LEFT highlights
these two molecules) and rotating or dragging affects theses two molecules.
Selecting molecules this way in essence deselects!
If I want to get my molecules online, while I can work around this small
bug, I cannot expect students on the web to do the same without being
told how.
Reinhold
------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
