Dear all,
having spend a couple of hours in reading the FAQ (e.g. http://salilab.org/modeller/FAQ.html#5 ), the manual (e.g.http://www.msg.ucsf.edu/local/programs/modeller/node29.html), this Mailinglist (e.g. http://salilab.org/archives/modeller_usage/2005/msg00143.html http://salilab.org/archives/modeller_usage/2003/msg00265.html ...) it is still a complete mystery to my how to fix the position of atoms when annealing.
It was suggested to simply DESELECT the atoms I do not want to move at all (http://salilab.org/archives/modeller_usage/2005/msg00155.html), but the link to the manual given did not made clear HOW TO deselect atoms. However, I made my way to http://www.msg.ucsf.edu/local/programs/modeller/node29.html (Refining only part of the model). Still, this did not help.
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!
>From the mailing-list I deduced, that quite a number of other people have been messing with the same question , and that referring to the manual or the F.A.Q doesn't really help. Instead, an example that does exactly what has been requested would be a pleasure!
Thank you very much in advance
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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SaTa