Shelxl-97: Help requested with omitted atoms and SWAT

Boyd Steere steere at
Thu Jul 30 18:50:32 EST 1998

Hello, all:

I am refining a protein with SHELXL-97-2 and wish to remodel a
poorly-traced loop of my structure.  I'm restarting the refinement
from the beginning with the atoms of that loop OMITted from my initial
model so that they will be ignored in the Fc calculation and the
refinement, with the intention of rebuilding the loop much later in
the refinement.
My concern is that these OMITted atoms will be considered part of the
solvent instead of part of the protein when SHELXL performs bulk
solvent correction with SWAT, and thereby have the density surrounding
them distorted.  In X-PLOR, I'd solve this problem by having including
the loop in the coordinates file used for making the solvent mask, but
I don't know how to solve this problem in SHELXL-97.  Any suggestions
would be greatly appreciated.  Thanks!


Boyd Steere  | Molecular Biology Institute, UCLA | steere at

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