Re: [Jmol-users] weird problem launching minimization

[Angel H. <ang...@ua...>]

This is the summary and a test case:

1. Problem is there only for local files, not from server. Seems to 
be related to Jmol reading text files (either scripts or the UFF.txt 
file embedded somehow inside Jmol) from a folder where the applet 
jars are but the webpage is not.

Main_folder
   |
    -- Pages_folder
          |
           -- mypage.htm
   |
    -- Jmol_folder
          |
           -- *.jar files
           -- Jmol.js
           -- model.mol
           -- test.spt

2. The problem shows for reading script files (that do no model 
loading, just simple commands) and also for running "minimize"

3. The same script commands or the minimize command work fine when 
issued from teh script console. It'sonly calling them from a 
jmolButton or an <input type="button" onClick="jmolScript()"> that 
causes the problem.

4. Same behaviour in 11.6, 11.8.24 and 12.0.RC17

5. Errors are like:

For loading a script file:

FileManager opening 
file:/F:/webs/_Proyectos/_pruebas/Jmol_local_scripts/Jmol-
12.0.RC17/halos.spt
script ERROR: script ERROR: 
io error reading 
file:/F:/webs/_Proyectos/_pruebas/Jmol_local_scripts/Jmol-
12.0.RC17/halos.spt: 
java.security.AccessControlException: 
access denied (java.io.FilePermission 
F:\webs\_Proyectos\_pruebas\Jmol_local_scripts\Jmol-
12.0.RC17\halos.spt read)

For running minimize:

Minimizing 17 atoms
minimize: initializing (steps = 100 criterion = 
0.0010000000474974513) ...
minimize: using org.jmol.minimize.forcefield.ForceFieldUFF
17 atoms will be minimized.
minimize: creating bonds...
minimize: setting atom types...
Couldn't find file: UFF.txt
Exception null in getResource UFF.txt
0 force field parameters read


Test case is avalable at
http://biomodel.uah.es/angel/test/Jmol_local_scripts.zip
Unzip and run from disk, not from server.
(Uses monolithic applet for simplicity; I've tested with the split 
applet too)