[Chimera-users] minimization error

[Eric Pettersen]

Hi Divya,
	In the 1.2422 release that you are using there is no "nsteps"  
keyword.  In that version it was called "steps".  The documentation  
that corresponds to your version is bundled with you version (use your  
Chimera's Help menu or type "help command-name" in its command line).   
Documentation on the web corresponds (depending on where you look)  
either to the current production release [1.5.3] or the current daily  
build [1.6].
	I would highly recommend that you upgrade to a current version of  
Chimera since many improvements have been made to the minimization  
code (and everything else really) since the 1.2422 build (which is  
more than 4 years old after all).

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Dec 1, 2011, at 11:09 AM, divya neelagiri wrote:

> Hello,
>
> I got this error when I was trying to minimize a structure. please  
> tell me what went wrong.
>
>
> Executing testchim.py...Opening test1_chimera.mol2...1 model opened
>
> Traceback (most recent call last):
>   File "/data/pgm/chimera/chimera_1.2422/share/__main__.py", line  
> 59, in ?
>     value = chimeraInit.init(sys.argv)
>   File "CHIMERA/share/chimeraInit.py", line 298, in init
>     chimera.openModels.open(a, prefixableType=1)
>   File "CHIMERA/share/chimera/__init__.py", line 1253, in open
>   File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython
>   File "testchim.py", line 10, in ?
>     rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze  
> none nogui true")
>   File "CHIMERA/share/chimera/__init__.py", line 1912, in runCommand
>   File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand
>   File "CHIMERA/share/MMMD/ChimeraExtension.py", line 29, in cmdMMMD
>   File "CHIMERA/share/Midas/midas_text.py", line 281, in  
> doExtensionFunc
>   File "CHIMERA/share/Midas/midas_text.py", line 1885, in _getRealKw
> MidasError: Keyword 'nsteps' doesn't match any known keywords
> Error while processing testchim.py:
> MidasError: Keyword 'nsteps' doesn't match any known keywords
> (see reply log for Python traceback info)
>
>
>
>
> This is my program. I tried to execute it from command line using
> chimera --nogui testchim.py
>
> import os
> import chimera
>
> from chimera import runCommand as rc
> from chimera import replyobj
>
> os.chdir("/data2/di/database_build/outputs/outputs_mol2_sdf")
> fn = "test1_chimera.mol2"
> rc("open " + fn)
> rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none  
> nogui true")
> rc("write format mol2 0 min/" + fn)
> rc("close all")
> rc("stop now")
>
>
>
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