Re: [modeller_usage] log files and processing multiple files

[Modeller Caretaker <>]

On 3/18/10 9:51 AM, abdullah ahmed wrote:
> 1) I do not get log files after running optimization. I am certain that
> it is not a matter of them taking really long to be made because I have
> been using Modeller for 3 months now and I have not gotten a log file. I
> do however, get "pdb.ini" "pdb.rsr" and "pdb.D000001" (contains info on
> maximal shift, energy changes and gradients).

You only get a log file if you use the 'mod9v7' script to run Modeller. 
If you run it in some other fashion, it will behave like a regular 
application and output the log to standard output, so you need to 
redirect it to a file.

e.g. at a Linux command line, the following commands do essentially the 
same thing:

mod9v7 foo.py
mod9v7 - < foo.py > foo.log
python foo.py > foo.log

If you are running your Python scripts on a Windows machine by simply 
double-clicking on them, the output will show up in a window and 
disappear when Modeller finishes. A better way to run these scripts is 
from a command line or the Python IDLE environment, so you can inspect 
the log output when Modeller finishes.

> 2) I have a series of molecules that I would like to apply the same
> constraints to, and then optimize. Is there a script I can use to
> optimize all the files in one go?

Modeller scripts are simply Python scripts so sure, you could write a 
simple Python script with a loop in it that runs over all of your molecules.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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