[phenixbb] Joint X-ray / neutron refinement

Sat Feb 24 05:56:33 PST 2024

Hi Kristoffer,

Are you running from the command-line? The current GUI in 1.21 does not
support joint refinement. We will release 1.21.1 to add support.

If you use the command-line, the presence of the xray and neutron scopes
will switch the parser to process the parameter file for joint xn
refinement. You should see a log that looks like

Starting phenix.refine
on Sat Feb 24 05:50:17 2024 by bkpoon
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found phil, params.eff

Processing PHIL parameters:

-------------------------------------------------------------------------------

  Adding PHIL files:

  ------------------
    params.eff

Switching to joint x-ray/neutron refinement mode

-------------------------------------------------------------------------------

The 1.21.1 release will probably be next week. I'm currently testing the
GUI. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org

On Fri, Feb 23, 2024 at 11:58 AM Tim Gruene <tim.gruene at univie.ac.at> wrote:

> Hello Kristoffer,
>
> maybe this is related to the first paragraph at the link that you
> provide ("The paradigm and implementation of the joint X-ray and
> neutron refinement were changed in the fall of 2023, as documented
> here: https://pubmed.ncbi.nlm.nih.gov/37942718/"):
>
> It is better  to use the information from an X-ray dataset via
> geometric restraints and refine against neutron data only (cf. DOI
> 10.1107/S1600576713027659), so that you focus on the information from
> the neutron data.
>
> Cheers,
> TIm
>
> On Fri, 23 Feb 2024 10:58:17 +0000 Kristoffer Lundgren
> <kristoffer.lundgren at compchem.lu.se> wrote:
>
> > Hello phenixbb,
> >
> > When trying to do joint refinement in phenix.refine 1.21-5207 using
> > the suggested joint_xn.eff file found at
> >
> https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement
> > as a template I get some error messages (running phenix.refine from
> > the command line):
> >
> >   Unrecognized PHIL parameters:
> >   -----------------------------
> >     xray.refinement.refine.strategy (file "joint_xn.eff", line 33)
> >     xray.refinement.main.simulated_annealing (file "joint_xn.eff",
> > line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff",
> > line 37) xray.refinement.main.number_of_macro_cycles (file
> > "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file
> > "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing
> > (file "joint_xn.eff", line 48)
> > neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line
> > 49) neutron.refinement.main.number_of_macro_cycles (file
> > "joint_xn.eff", line 50)
> >
> > Can you please advice on how to proceed? It looks like the options
> > supplied are not recognized at all by phenix.refine.
> >
> > Best regards
> > Kristoffer
> >
> >
> > From: <phenixbb-bounces at phenix-online.org> on behalf of Derek Logan
> > <derek.logan at biochemistry.lu.se> Date: Monday, 22 January 2024 at
> > 09:39 To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
> > Cc: Ulf Ryde <ulf.ryde at compchem.lu.se>, "esko.oksanen_ess.eu"
> > <esko.oksanen at ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray /
> > neutron refinement
> >
> > Hi phenixbb,
> >
> > I'm trying to understand the current status of joint X-ray/neutron
> > refinement in phenix.refine. The announcement of the latest release
> > mentions a change in the algorithm as described in the recent
> > publication. In the documentation:
> >
> > Structure refinement in
> > PHENIX<
> https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement
> >
> > phenix-online.org<
> https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement
> >
> >
> > [AURqZhI53yp3gAAAABJRU5ErkJggg==]<
> https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement
> >
> >
> >
> >
> > it's described how you can run joint refinement using a parameter
> > file. Does this mean that it is *only* possible in this way and not
> > through the GUI? The GUI was very useful in the past as it
> > automatically opened Coot with the maps for both X-rays and neutrons,
> > and the refinement statistics for both were displayed in the GUI. As
> > far as I can see joint refinement via the GUI last worked in version
> > 1.19.2-4148 from 2021.
> >
> > Best regards
> > Derek
>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
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