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:

https://www.phenix-online.org/download/nightly_builds.cgi?show_all=1

Let me know of any issues!

Good luck,
Pavel

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

Hi!

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.

Cheers,

Jens