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