Re: [Chimera-users] Unrecognized command: "minimize"

18 Aug 2011


      Hi Viachaslau,
     I think the problem is that you got the command spelling wrong.  It 
should be "minimize", not "miminize" :-)

-- scooter

On 08/18/2011 01:54 AM, Viachaslau Bernat wrote:
...
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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Re: [Chimera-users] Unrecognized command: "minimize"

Scooter Morris