[cctbxbb] probe/reduce repositories

[Hattne, Johan]

> 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
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