This is the Java console: FileManager opening F:/webs/_Proyectos/_pruebas/Jmol/Jmol- minimize/thyroxine.cml
FileManager.openFile(F:/webs/_Proyectos/_pruebas/Jmol/Jmol-
minimize/thyroxine.cml) //F:/webs/_Proyectos/_pruebas/Jmol/Jmol-
minimize/thyroxine.cml
FileManager opening F:\webs\_Proyectos\_pruebas\Jmol\Jmol-
minimize\thyroxine.cml
The Resolver thinks cml(xml)
openFile(F:/webs/_Proyectos/_pruebas/Jmol/Jmol-
minimize/thyroxine.cml)282 ms
ModelSet: haveSymmetry:false haveUnitcells:false
haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
ModelSet: not autobonding; use forceAutobond=true to force automatic
bond creation
eval ERROR: org.jmol.minimize.Minimizer
----line 1 command 1 of file null:
>> minimize <<
OK, so while the 11.5.21 app is not working, I downloaded 11.5.22_dev
applet from Bob's site and tested it (the Jmol.jar there is older).
I may be being too ambitious, but it runs the minimization nicely
except for the aromatic rings, which are not flat.
The starting model is 2D.
I also tried adding the aromatic commands as in Bob's caffeine
example, but the result is the same.
I've tried to attach a zipfile with the starting file, thyroxine.cml,
and the resulting coordinates as exported by Jmol, but my mail server
is blocking the zipfile. Now trying again unzipped and sending it off-
list to Bob.
Hope it is of help.
I have tried other molecules with the same problem, but e.g. a flat
caffeine from PubChem works better, the aromatic ring comes out
nearly flat, particualrly after repeating the minimization.
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---- File information -----------
File: thyroxine_result1.mol
Date: 27 Mar 2008, 23:59
Size: 1533 bytes.
Type: Unknown
thyroxine_result1.mol
Description: Binary data
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prepared for transmission using the Internet MIME message format.
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---- File information -----------
File: thyroxine.cml
Date: 25 Mar 2006, 14:23
Size: 3795 bytes.
Type: Unknown
thyroxine.cml
Description: Binary data
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