[phenixbb] unrestrained refinement

Kaiser, Jens T. kaiser at caltech.edu
Mon Jan 28 17:00:45 PST 2019

Thanks, Pavel!

I'll let you know how it goes.



From: Pavel Afonine <pafonine at lbl.gov>
Sent: Monday, January 28, 2019 4:58:22 PM
To: Kaiser, Jens T.; phenixbb at phenix-online.org
Subject: Re: [phenixbb] unrestrained refinement

Hi Jens,

I re-enabled this functionality so that phenix.refine can continue if there is an unknown entity found in input model file.
To run unrestrained refinement you can simply use "wc=0" which sets zero weight on geometry restraints (this is unrelated to above).

A next available nightly build should have it:


Let me know of any issues!

Good luck,

On 12/18/18 14:58, Kaiser, Jens T. wrote:


  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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