[phenixbb] unrestrained refinement

Kaiser, Jens T. kaiser at caltech.edu
Tue Dec 18 14:58:46 PST 2018


  I'm trying to do unrestrained refinement of a small molecule in phenix. I have done this many years ago, but it seems whatever I try, phenix.refine now complains about missing nonbonded energy type for all atoms.

 The pdb file I supply has the following format (just one line)

HETATM   33  C81 UNK     1       3.117  14.425  18.765  1.00  1.45           C

I tried unchecking all references to geometry restraints in the GUI, setting wc and wu to 0

  I also started from a default .eff file and set all references to restraints to either True of False (depending what they said).

  I also tried the line from the phenix.refine documentation:

phenix.refine ../cif_in/mkt_a.ent ../data/181119/proc/137C3/XDS_17000.HKL strategy=individual_sites wc=0 refinement.input.symmetry_safety_check=warning refinement.input.xray_data.r_free_flags.generate=True

 I'm using phenix v 1.14-3260 from an sbgrid environment.

  Any pointers welcome.


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