[cctbxbb] probe/reduce repositories

[Billy Poon]

Hi Johan,

You should probably just download the latest Phenix source, either from our
repositories or a nightly build, and compile a new copy. That should
provide you with all the modules and dependencies.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Wed, May 3, 2017 at 12:55 PM, Hattne, Johan <hattnej at janelia.hhmi.org>
wrote:

> Not really installing.  It’s an installation from 2011 that has been moved
> across the US and kept up-to-date (of sorts) by svn update and more
> recently git pull.
>
> // J
>
> > On May 3, 2017, at 15:47, Billy Poon <bkpoon at lbl.gov> wrote:
> >
> > Hi Johan,
> >
> > How are you installing Phenix? The phenix builder for bootstrap.py
> (PhenixBuilder class) automatically includes probe and reduce.
> >
> > --
> > Billy K. Poon
> > Research Scientist, Molecular Biophysics and Integrated Bioimaging
> > Lawrence Berkeley National Laboratory
> > 1 Cyclotron Road, M/S 33R0345
> > Berkeley, CA 94720
> > Tel: (510) 486-5709
> > Fax: (510) 486-5909
> > Web: https://phenix-online.org
> >
> > On Wed, May 3, 2017 at 12:21 PM, Hattne, Johan <hattnej at janelia.hhmi.org>
> wrote:
> >
> > > On May 3, 2017, at 11:40, Hattne, Johan <hattnej at janelia.hhmi.org>
> wrote:
> > >
> > > Dear all;
> > >
> > > I appear to be missing probe in my source build.  On running
> phenix.model_vs_data I get the traceback posted below.  The error message
> appears to be a tad misleading, because having probe in PATH is not enough:
> the actual test in the code is
> > >
> > >  if (not libtbx.env.has_module(name="probe")):
> > >
> > > which leads me to believe that I’m supposed to have something
> probe-like in my source tree, but the duke-server I used to get these kinds
> of things from (quidditch?) seems unresponsive from here.  This is the
> first time in weeks that I’m doing this, so it is very much likely that
> whatever happened to break my setup happened quite some time ago.
> > >
> > > Cluebat, anyone?
> > >
> > > // Cheers; Johan
> > >
> > > Traceback (most recent call last):
> > >  File "/mnt/gonen/home/hattnej/projects/phenix-build/../
> phenix-src/phenix/phenix/command_line/model_vs_data.py", line 6, in
> <module>
> > >    show_geometry_statistics = True)
> > >  File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_
> project/mmtbx/model_vs_data.py", line 710, in run
> > >    atom_selections          = atom_selections)
> > >  File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_
> project/mmtbx/model_vs_data.py", line 346, in show_geometry
> > >    restraints_manager = restraints_manager)
> > >  File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_
> project/mmtbx/model_statistics.py", line 138, in __init__
> > >    molprobity_scores=molprobity_scores)
> > >  File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_
> project/mmtbx/model_statistics.py", line 51, in __init__
> > >    self.clashscore = clashscore(pdb_hierarchy=pdb_
> hierarchy).get_clashscore()
> > >  File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_
> project/mmtbx/validation/clashscore.py", line 90, in __init__
> > >    "http://kinemage.biochem.duke.edu/")
> > > RuntimeError: Probe could not be detected on your system.  Please make
> sure Probe is in your path.
> > > Probe is available at http://kinemage.biochem.duke.edu/
> >
> > For the benefit of anybody else running into this: probe is at
> https://github.com/rlabduke/probe.git, reduce at
> https://github.com/rlabduke/reduce.git.
> >
> > // Johan
> >
> >
> >           Research Specialist @ Gonen Lab
> > ____________________________________________________
> >     Janelia Research Campus * 19700 Helix Drive
> > Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
> >
> >
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> > http://phenix-online.org/mailman/listinfo/cctbxbb
> >
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>
>           Research Specialist @ Gonen Lab
> ____________________________________________________
>     Janelia Research Campus * 19700 Helix Drive
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
>
>
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