Re: [modeller_usage] HowTo Fix Position of Atoms?

[Modeller Caretaker <>]

SaTa wrote:
> having spend a couple of hours in reading the FAQ (e.g.
> http://salilab.org/modeller/FAQ.html#5 )

You seem to be confused between atom selections and restraints (that FAQ 
is for adding or removing restraints, not atoms). Modeller only 
optimizes selected atoms. Alternatively, you could have it optimize all 
atoms, but add restraints to try and stop some of them from moving. In 
your situation the first solution is perhaps more appropriate.

> the manual
> (e.g.http://www.msg.ucsf.edu/local/programs/modeller/node29.html),

I don't know where you got that link from; the official Modeller manual 
is at http://salilab.org/modeller/manual/. But yes, "refining only part 
of the model" is what you want to do:
http://salilab.org/modeller/manual/node29.html

> I simply do not understand how to realize this:
>
> Do Not Move The Position Of The Atoms Of Residue 75 to 80 in All
> Chains!

Obviously, you select all residues _except_ 75 to 80.

> > From the mailing-list I deduced, that quite a number of other
> > people have been messing with the same question

The links you posted are related to entirely different problems 
(absolute position restraints are used to restrain atoms to planes, 
lines or points, but not to fix them, while ligand restraints are 
automatic).

> > Instead,
> > an example that does exactly what has been requested would be a
> > pleasure!

I can't give you an example that does "exactly what has been requested" 
because you didn't give the exact problem. But let's assume you're 
modeling a single chain protein with 100 residues, numbered 1 to 100. In 
this case, because we don't want residues 75 to 80 to move, we select 
residues 1-74 and 81-100, so we simply modify the select_atoms routine 
given in the manual (linked above) to:

    def select_atoms(self):
        self.pick_atoms(selection_segment=('1:', '74:'),
                        selection_search='segment', pick_atoms_set=1,
                        res_types='all', atom_types='all',
                        selection_from='all',
                        selection_status='initialize')
        self.pick_atoms(selection_segment=('81:', '100:'),
                        selection_search='segment', pick_atoms_set=1,
                        res_types='all', atom_types='all',
                        selection_from='all',
                        selection_status='add')

	Ben Webb, Modeller Caretaker
--
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