Re: [Jmol-users] Jmol version 10 prerelease 17 & script

[Old Address]

Miguel wrote:
Jan,
 

Hi Miguel,
yes I did
ant clean main
and tied again with 10pre17 and the problem persists:
$ ./jmol --script ../tst
/usr/bin/egrep: 1: Syntax error: redirection unexpected
   

Q: What is this call to egrep?
 

this is not important (it is in the jmol sh script included in the cvs:
while [ `echo $1 | egrep '^-D' | wc -l` != 0 ]; do
)
 

splash_image=jar:file:/D:/Jmol/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg
using Smarter Model Adapter
(C) 2004 The Jmol Development Team
Jmol Version 10pre17  2004/11/16 01:42
java.vendor:Sun Microsystems Inc.
java.version:1.5.0-rc
os.name:Windows XP
User macros dir: C:\Dokumente und Einstellungen\j\.jmol\macros
      exists: false
 isDirectory: false
Executing script: ../tst
animationReplayMode=0
animationReplayMode=0
FileManager.openFile(../pdb1izl.ent)
The Jmol Console report:
SmarterJmolAdapter:The Resolver thinks:Pdb
openFile(../pdb1izl.ent) 890 ms
I see someone who does not have a carbonyl oxygen
I see someone who does not have a carbonyl oxygen
and the Rasmol Scripts console:
ScriptException:bad argument count
   Script line:vector 0,050
ScriptException:bad argument count
   Script line:vector 0,050
$
   

This looks like your script is using commas instead of dots as the decimal
separator.
 vector 0.050
 

the script ../tst does only contain the following two commands:
zap
load pdb ../pdb1izl.ent
 

though, with the simple tst script, the graphics window looks OK, it
isn't. This could be proved by adding some rendering commands (which are
not executed) or by executing:
script ../tst
ScriptException:RasMol virtual machine error - stack underflow
   Script line:frame 1
ScriptException:RasMol virtual machine error - stack underflow
   Script line:frame 1
ScriptException:RasMol virtual machine error - stack underflow
   Script line:frame 1
$
   

Send me your test script and your entry files.
 

I downloaded the pdb1izl.ent direct from the PDB and the coordinate part 
didn't contain any ',', furthermore script and PDB file had run well 
with an older Jmol version.
Regards, Jan

Miguel
 


zap
load pdb ../pdb1izl.ent