Hi Jens, let us know if you manage to make it work. If not I can change phenix.refine to not care about restraints at all if unrestrained refinement is requested (currently it still constructs restraints no matter what just to report geometry statistics such as bond/angle rmsd etc; but this can be changed.). This may take me a day to do. Pavel On 12/18/18 18:54, Nigel Moriarty wrote:

Jena

UNK is, surprisingly, not a complete unknown. It is a general amino acid used for unknown amino acids. Your model contains a C81 atom which is not in the UNK restraints.

However, regardless of the existence of UNK or not, you need to provide the refinement with a restraints file whether automatically or user supplied. It is needed for the atom types and non-bonded interactions so it should contain an atom loop and a bond loop.

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709     Email : [email protected] Fax   : 510-486-5909       Web  : CCI.LBL.gov http://CCI.LBL.gov

On Tue, Dec 18, 2018 at 3:01 PM Kaiser, Jens T. mailto:[email protected]> 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

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Thanks, Pavel! I'll let you know how it goes. Cheers, Jens ________________________________ From: Pavel Afonine Sent: Monday, January 28, 2019 4:58:22 PM To: Kaiser, Jens T.; [email protected] 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: 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