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 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 wrote:

...

On May 3, 2017, at 11:40, Hattne, Johan 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 [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

All appears to be fine now, thanks a lot Billy! // J

On May 3, 2017, at 19:01, Billy Poon wrote:

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 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 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 wrote:

...

On May 3, 2017, at 11:40, Hattne, Johan 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 [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376