[phenixbb] unrestrained refinement

Pavel Afonine pafonine at lbl.gov
Tue Dec 18 20:42:13 PST 2018


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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov <http://CCI.LBL.gov>
>
>
> On Tue, Dec 18, 2018 at 3:01 PM Kaiser, Jens T. <kaiser at caltech.edu 
> <mailto:kaiser at caltech.edu>> 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
>
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://phenix-online.org/mailman/listinfo/phenixbb
>     Unsubscribe: phenixbb-leave at phenix-online.org
>     <mailto:phenixbb-leave at phenix-online.org>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20181218/af415c90/attachment.htm>


More information about the phenixbb mailing list