Hi,
The Modeller objective function value does not necessarily indicate the
model quality. It is more a measure of how well the model satisfies the
restraints used to calculate it. The lower the value the better the
satisfaction of restraints is. You can use external evaluation methods
(like Procheck or ProsaII) that sometimes give a better indication of
the model quality. But these methods are mostly useful for comparing
models based on different templates and/or alignments. You could proceed
in the following way:
1. Build models based on an initial alignment and select the one with
the
best (lowest) modeller objective function value.
2. Evaluate this model with external methods.
3. If errors are detected change the alignment (or template) and got to
1.
Now with respect to Procheck. Usually models build with Modeller will
have good stereochemistry because it is part of the restraints used to
calculate the model (CHARMM potentials). When you observe stereochemical
violations in your model it usually means that something is wrong with
the alignment in that region or (more rare) with the optimization. You
could try to do a more thorough optimization of you model by setting
MD_LEVEL = 'refine1' before calling the 'model' routine in your TOP
file. If the violations don't disappear try alternative alignments for
that particular region.
I hope this helps.
Best Wishes,
Roberto
--
Roberto Sanchez | phone : (212) 327 7206
The Rockefeller University | fax : (212) 327 7540
1230 York Avenue, Box 38 | e-mail:
New York, NY 10021-6399 | http://salilab.org
DEBASHIS MUKHOPADHYAY wrote:
>
> Dear Modellers,
>
> It appears that I have successfully modelled a mutated protein using
> 'model.top' routine which generated 20 output co-ordinates to choose
> from. It is noted that each file contains a parameter called MODELLER
> OBJECTIVE FUNCTION - most possibly indicating the model quality(?).
> Now, the question is which value of the function to consider - the
> lowest one or vice versa?
>
> Also, when I checked the secondary str. etc. of one such model using
> PROCHECK, several bad contacts were noted. Can you suggest any
> particular 'top' routine which will eventually eliminate all these / or
> optimize them, so as to make the model acceptable?
>
> Thanks in advance.
>
> Debashis