Re: [modeller_usage] R: error in using mutate_model
To: Anna Marabotti <>
Subject: Re: [modeller_usage] R: error in using mutate_model
From: Modeller Caretaker <>
Date: Wed, 24 Mar 2010 14:52:59 -0700
Cc:
On 3/24/10 9:57 AM, Anna Marabotti wrote:
thank you for your comments. You are true, on my machine I have Python
3.0.1. However, Modeller seems to work in any case, since I was able to
model a protein with the automodel procedure sometime ago. Moreover,
yesterday I found a way to use the wiki script mutate_model.py: I started
from the launch screen of Modeller and typed:
mod9v7 mutate_model.py my_modelname my_respos my_resname my_chain>
my_log.log
Right - the mod9v7 binary includes a copy of Python 2.3 for your
convenience, so it will work on machines that don't have Python
installed. But (unlike Python itself) you can't "import" any
non-Modeller Python modules in your Python scripts, other than the
built-in 'sys' module.
I finally obtained my mutants. I had a look at them and they seem to be
correct; the only strange things are: i.in the PDB file, the atoms of the
new sidechain introduced by the program do not have the B-factor (I don't
remember if this was true also previously)
Modeller uses B-factor to record the value of the scoring function. It
is not really comparable with the crystallographic B-factor. So even if
the new atoms had the B-factor, it wouldn't make a lot of sense.
ii. mutate_model.py launched in
this way does not produce the my_log.log file, but the mutate_model.log
file.
Right - the mod9v7 script produces a .log file with the same name as
your input Python file. If you want to name the file yourself, you can
ask the script to use standard input and output and redirect them yourself:
Finally, a little suggestion: probably it would be better to rename the wiki
script in another way, since two MODELLER have the same name: the wiki
script mutate_model.py and the command mutate_model.py that inserts
mutation, but without the whole mutant sidechain optimization by conjugate
gradient and MD.