On Mon, Sep 27, 2004 at 04:18:42PM +0300, vivek sharma wrote:
> 1. Is the value of objective function obtained after complete process of
> MODELER , system size specific? I mean when I model a system of > 500
> residues (target), it generates >50000 restraints (3 templates used) and
> final value of objective function is >20000, but when I model a part of
> the target , taking respectively aligned template portions, approx 150
> residues (target), the restraints generated are around 9000 and final
> value of objective function comes to 2000 units.
> So, this shows that smaller the system , lower the final value of
> objective function, same restraints selected in both cases and assume no
> violations. Please comment
The objective function is determined purely by your restraints (static
and dynamic). If you have a different number or type of restraints for
your two systems, the objective function scores are not comparable.
> 3. Thirdly, from documentation I came to understand that, that when one
> wants to generate non bonded pair restraints as static ones, he has to
> include them in MAKE_RESTRAINTS command and keep all DYNAMIC_SPHERE,
> LENNARD, COULOMB, etc off. Can you tell me which is better , non bonded
> restraints used as static or non bonded restraints as dynamic (generated
> automatically by MODELER on fly)?
See http://salilab.org/modeller/manual/node101.html
It is usually better to use dynamic restraints because then Modeller can
use a nonbond pair list to reduce execution time.
Ben Webb, Modeller Caretaker
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