Dear Chimera developers,

I've got a problem with scripting in chimera. By analogy with your example I've written a python script for geometry optimization of small library of ligands. In GUI mode all commands run smoothly as I type them into chimera command line. Nevertheless, when I try to run a script containing the same commands I get the error `unrecognized command: "minimize"`, no matter if I run it from GUI interface menu or with --nogui parameter.

Here is my testing script (test.py):

 import os
 import chimera
 from chimera import runCommand as rc
 from chimera import replyobj
 os.chdir("/home/viachaslau/sybyl/sublib/")
 fn = "lib1.mol2"
 rc("open " + fn)
 rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true")
 rc("write format pdb 0 min/" + fn + ".pdb")
 rc("close all")
 rc("stop now")

And here is the output from Python:

~/sublib> ~/chimera/bin/chimera --nogui test.py
Executing test.py...
Opening lib1.mol2...
UNQ1 opened

Traceback (most recent call last):
  File "/home/viachaslau/chimera/share/chimeraInit.py", line 677, in init
    chimera.openModels.open(a, prefixableType=1)
  File "/home/viachaslau/chimera/share/chimera/__init__.py", line 1541, in open
    models = func(filename, *args, **kw)
  File "/home/viachaslau/chimera/share/chimera/__init__.py", line 973, in _openPython
    loadFunc(sandboxName, fileName, f)
  File "test.py", line 8, in <module>
    rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true")
  File "/home/viachaslau/chimera/share/chimera/__init__.py", line 2235, in runCommand
    makeCommand(*args, **kw)
  File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand
    'Unrecognized command: "%s"' % cmd
MidasError: Unrecognized command: "miminize"
Error while processing test.py:
MidasError: Unrecognized command: "miminize"

  File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand
    'Unrecognized command: "%s"' % cmd

See reply log for Python traceback.

I run SUSE 11.3 as operating system and chimera is installed into ~/chimera/
I also tried to run commands row by row in IDLE window of chimera and found out that python suspends on runCommand("minimize ...") command

-- 
Viachaslau Bernat, PhD-student
Department Chemistry and Pharmacy
Schuhstrasse 19, 91052 Erlangen – Germany
Phone: +49-9131-8522588
www.medchem.uni-erlangen.de

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