Jayashankar wrote:
Dear ccp4bb and Paul emsley,
I have a problem in coot,
I could clearly see the density for some small molecule that was
present in the sample buffer. when I generate .cif from monomer sketch
library from ccp4 and use same .cif
in coot for real space refinement, the small molecule goes back and
sit into the nearby protein density rather than to stay in the
speculated density for that molecule.
i can very well regularize the zone but could not do any real space
refinement of that small molecule.
What might be the problem?
Dear Jayashankar,
First you need to check that the map against which you are refining is
the correct one.
(Model/Fit/Refine -> Select Map).
If that doesn't work, try masking out the protein. (Let's presume that
the surrounding protein atoms are in the A chain and the small molecule
is not in the A chain):
Extensions -> Mask Map by Atom Selection
with selection "//A/"
Now change the refinement map to "Generic Masked Map" using Select Map.
Now refine again.
That should work.
HTH,
Paul.
