Re: [Jmol-users] Jmol v10pre8

[Jan R. <jr...@im...>]

Miguel schrieb:

>Judith & Egon wrote:
>
>  
>
>>>The double dash does not work either.  When I use the double dash as
>>>you suggest, I get the error message I was getting using the -script in
>>>10pre7 instead of the unrecognized file format message:
>>>      
>>>
>>I think the --script *does* work... see below:
>>    
>>
>
>[snip]
>
>  
>
>>Here's the statement that the --script is loaded and being run...
>>I did not see this line in your previous output.
>>*But*:
>>
>>    
>>
>>>uncaught exception: java.lang.NullPointerException: string is null
>>>java.lang.NullPointerException: string is null
>>>         at sun.java2d.SunGraphics2D.drawString(SunGraphics2D.java:2821)
>>>         at org.openscience.jmol.app.Splash.showStatus(Splash.java:98)
>>>         at org.openscience.jmol.app.Jmol.main(Jmol.java:394)
>>>      
>>>
>>This seems to be a bug Jmol elsewhere... I had this problem too, but is
>>not
>>in the '--script' code...
>>    
>>
>
>I cannot reproduce this problem on either Linux or Win32.
>
>Egon, can you take a look at it?
>
>
>Miguel
>
>  
>
using the following jmolscript.bat on XP I configured Mozilla to connect 
the MIME type:
application/x-jmol
(IE extension .JMZ)
with jmolscript.bat which must be in the same DIR as Jmol.jar

@echo %CMDCMDLINE%
@set THISPGM=%~s0
@set JMZ=%~s1
@set JMOLPATH=%THISPGM:~0,-13%
@set PATH=%JMOLPATH%;%PATH%
@cd %JMOLPATH%
java -jar Jmol.jar --script %JMZ%

sometimes the Jmol application starts and executes the script as 
intended but sometimes it fails. But if it fails, doing a
 script URL
or
 script TEMP/FILE.JMZ
on the Jmol scripting console succeeds, thus the script is OK.

e.g.
http://www.imb-jena.de/cgi-bin/rascript.exe?TYPE=Jmol&CODE=3cro

C:\Jmol>java -jar jmol.jar --script 
C:\DOKUME~1\root\LOKALE~1\Temp\3CRO_J~1.JMZ

using Smarter Model Adapter
(C) 2004 The Jmol Development Team
Jmol Version 10pre8  2004/03/28 20:31
java.vendor:Sun Microsystems Inc.
java.version:1.4.2_04
os.name:Windows XP
JmolViewer.setShapeProperty(Labels,color,null)
propertyName=color
value=null
JmolViewer.setShapeProperty(Sticks,color,null)
propertyName=color
value=null
Graphics3D.setSize(640,10)
getting ready to allocateBuffers
returning from Graphics3D.setSize()
Graphics3D.setSize(488,427)
getting ready to allocateBuffers
returning from Graphics3D.setSize()
Executing script: C:\DOKUME~1\root\LOKALE~1\Temp\3CRO_J~1.JMZ
uncaught exception: java.lang.NullPointerException: string is null
java.lang.NullPointerException: string is null
        at sun.java2d.SunGraphics2D.drawString(Unknown Source)
        at org.openscience.jmol.app.Splash.showStatus(Splash.java:98)
        at org.openscience.jmol.app.Jmol.main(Jmol.java:394)

this time, it failed (I had 3 successful tries - with other codes with 
Mozilla before, and the Jmol instances were still open)
but doing a
 script C:\DOKUME~1\root\LOKALE~1\Temp\3CRO_J~1.JMZ
on the scripting console of this new Jmol instance succeed.

now I did this with IE
http://www.imb-jena.de/cgi-bin/rascript.exe?CODE=3cro&TYPE=Jmol
and succeed

C:\Jmol>java -jar jmol.jar --script 
C:\DOKUME~1\root\LOKALE~1\TEMPOR~1\Content.IE5\OPEF4TUV\3CRO_J~1.JMZ
using Smarter Model Adapter
(C) 2004 The Jmol Development Team
Jmol Version 10pre8  2004/03/28 20:31
java.vendor:Sun Microsystems Inc.
java.version:1.4.2_04
os.name:Windows XP
JmolViewer.setShapeProperty(Labels,color,null)
propertyName=color
value=null
JmolViewer.setShapeProperty(Sticks,color,null)
propertyName=color
value=null
Graphics3D.setSize(640,10)
getting ready to allocateBuffers
returning from Graphics3D.setSize()
Graphics3D.setSize(488,427)
getting ready to allocateBuffers
returning from Graphics3D.setSize()
Executing script: 
C:\DOKUME~1\root\LOKALE~1\TEMPOR~1\Content.IE5\OPEF4TUV\3CRO_J~1.JMZ

and after restarting Mozilla 3cro failed again but after successfully 
trying 1plc, 3cro succeed ???
C:\Jmol>java -jar jmol.jar --script 
C:\DOKUME~1\root\LOKALE~1\Temp\3CRO_J~2.JM

using Smarter Model Adapter
...
Executing script: C:\DOKUME~1\root\LOKALE~1\Temp\3CRO_J~2.JMZ
display modelID=0
JmolViewer.setShapeProperty(Measures,clear,null)
propertyName=clear
value=null
FileManager.openFile(http://www.imb-jena.de/cgi-bin/Piet/PDBsend.pl?code=3cro)

Regards, Jan