[phenixbb] Ligandfit problems with ligand geometry

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Sep 10 11:56:52 PDT 2009

Hi Kendall,
No, ligandfit finds the core of your ligand, then traces the remainder, 
rotating torsion angles for the ligand using a simple algorithm.  It does
this several times, and the pieces are stitched together.  No refinement
is done. This can yield poor geometry as you found. The best solution is
to then refine the model+ligand together. Usually that will take care of
the poor ligand geometry.
All the best,
Tom T

>> I just tried ligandfit for the first time and it did not maintain proper
>> geometry of the ligand. There were problems with both bond lengths and
>> planarity. Is there a way to specify a .cif file? The ligand pdb was
>> generated with PROGRD2, and I have had good success refining a structure
>> that contains a very close analog with phenix.refine.
>> Kendall Nettles
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>> phenixbb at phenix-online.org
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