(none)

Jiang Jiansheng jiang at LAPLACE.CSB.YALE.EDU
Sun Jul 23 13:21:22 EST 1995



> I am using xplor to refine a protein, and there is a large peak from fo-fc map that
> is right on a 3-fold axis.  I want to place an atom here to model this peak, but when
> I do, by symmetry, I have 3 atoms all very close to each other, and xplor dies when i do
> refinement.  I have tried setting the occupancy to 1/3, but i get the same result.  Is there
> some way to turn off the interactions between model and symmetry?
> 

> thanks for any suggestions
> 

> Matt Pugmire
> pugmire at bio.cornell.edu


This is indeed an FAQ.  Similar questions about
the special position refinement were asked and answered in the
previous mailing messages (look at the archive).

Now I am trying to summarized as follows: 


1. If the atoms at the special positions are mostly rigid,
just fix them by using

  CONSTRAINTS FIX=(special-atoms) END

which turns off all interactions for the special atoms.

2. If the atoms lie exactly on the special symmetry axis
and there is NO any bond to other atoms, try to turn off the 

self-interactions for special atoms by using

  CONSTRAINTS 

    INTERACTION ( NOT (special-atoms) ) ( NOT (special-atoms) )
  END  


3. If the atoms lie exactly on the special symmetry axis
and there are bonds to other atoms, try to turn off the 

self-interactions and symmetry-related interactions
for special atoms by using

  CONSTRAINTS 

    INTERACTION ( NOT (special-atoms) ) ( NOT (special-atoms) )
       WEIGHT * 1. END
    INTERACTION ( special-atoms ) ( NOT (special-atoms) )
       WEIGHT * 1. PVDW 0. PELE 0. END
  END  


4. The special atoms have to be on the special positions
precisely.  If not, try to move the atoms into the positions
on the graphics.  For special molecules/groups (like SO4, PO4)
locating on the symmetry axis, one has to re-construct the
"asymmetry" unit (topologically) for them (please refers to 

Gerard Kleywegt's email on June 15, 1995).

5. NOTE: X-PLOR will check and produce the occupancy factor for
the atoms those are exact on the special position, no matter what
the input occupancy is.

Jiansheng Jiang.
 





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