[cctbxbb] probe/reduce repositories

Billy Poon bkpoon at lbl.gov
Wed May 3 12:47:28 PDT 2017


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
>
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20170503/989396a2/attachment.htm>


More information about the cctbxbb mailing list