[Chimera-users] Unrecognized command: "minimize"

[Scooter Morris]

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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> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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