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Jiang Jiansheng jiang at LAPLACE.CSB.YALE.EDU
Thu Jul 6 14:32:36 EST 1995

> 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 }

   inter = (store7) (store7)
   inter = (store7 or store6) (store6)
   inter = (store7 or store5) (store5)

Jiansheng Jiang.



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