[phenixbb] Dealing with malformed ligand geometries in phenix.refine

Francis E Reyes Francis.Reyes at Colorado.EDU
Fri Aug 26 08:03:35 PDT 2011

Hi all

I've got 3.0A data and I'm ending up with distorted ligand geometry in phenix.refine. The model is complete and fitting the ligand is the final step (refined with individual_sites and individual_sites_real_space as suggested by an earlier posting). I've tried with a wxc_scale of 0.001 and it still looks wonky (tetrahedral C's not being so, etc). 

My cif is coming from phenix's internal db. 

Any suggestions?


Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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