Dear All,
I have a problem while refining (using refmac5) the structure with ligand in
2.5A resolution data.
After restraint refmac refinement, I tried to fit the ligand molecule into
the difference map. For this purpose, I created the substrate lib file using a
pdb file from PRODRG in the ccp4 sketcher and used the coot for fitting the
ligand.
Real space refinement works well after inserting the ligand into the
difference map. After real space refinement, I tried the refmac restraint
refinement with ligand. But the entire ligand molecule is coming out from the
electron density after refinement. But I didnt get any warning in the refmac
log file after refinement and it got terminated normally. Kindly let me know
the real problem if anybody knows. It would be great to finish my structure
refinement.
Thanks in Advance
Cheers,
Sampath
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