> I am trying to refine a protein structure where some of the side
> chains have 2 possbile configurations, ie. I would like to refine
> the occupanices of these 2 possible positions. Does anyone have any
> suggestions on this? So far, I have tried building in the 2nd position
> of a residue, then refining the occupancies. This seems to work, but when
> I try to do any kind of further positional refinement of the protien, there
> are too many bad contacts and it dies. There are bad contacts because the 2nd
> position of the residue is obviously close to the first, etc. I don't
> see any way around this. Any help would be appreciated
>
> Matt Pugmire
>pugmire at bio.cornell.edu
This is an FAQ question?
In subsequent refinements after building the 2nd comformations
one has to exclude all interactions between the two configurations.
Try the following:
{* define interactions which exclude interactions between two conformations *}
vector ident (store7) (segid "A" or segid "B") { all single conformation }
vector ident (store6) (segid "A1" or segid "B1") { all ALTernative 1 }
vector ident (store5) (segid "A2" or segid "B2") { all ALTernative 2 }
constraints
inter = (store7) (store7)
inter = (store7 or store6) (store6)
inter = (store7 or store5) (store5)
end
Jiansheng Jiang.
