[phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH; problem fixed.

Mooers, Blaine H.M. (HSC) Blaine-Mooers at ouhsc.edu
Tue Mar 14 11:23:16 PDT 2017


Hi Andy,

Thank you for the clarification!

Yes, I was wrong. There is still a tools subdirectory at the top level.

I installed the latest version of Rosetta from source.
This is version 3.8,  the Feb. 25th, 2017 release.
The rosetta\_options.py file is in the same location: main/source/src/apps/public/ERRASER.

Following up on your suggestion, I edited the file erraser.py in
/Applications/phenix-dev-2686/modules/phenix/phenix/erraser
by replacing line 543 with the following:

file_path = os.path.join(params.directories.rosetta_path, 'main/source/src/apps/public/ERRASER')

Phenix.erraser now runs.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Faculty webpage<http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d->   X-ray lab (LBSF)<http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStructureandFunction.aspx>   Molecular Graphics<https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/moleculargraphicslinks.html> Links <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/MolecularGraphicsLinks.html>  Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0>
office: (405) 271-8300   lab: (405) 271-8313   e-mail:  blaine-mooers at ouhsc.edu
________________________________
From: Andy Watkins [andy.watkins2 at gmail.com]
Sent: Tuesday, March 14, 2017 11:53 AM
To: Mooers, Blaine H.M. (HSC)
Subject: Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH

Yes, while the tools directory should still exist, the new path to ERRASER is in fact main/source/src/apps/public. I wonder if the issue lies in Phenix's subsequent interpretation of that environment variable -- i.e., the Phenix code is appending "tools/ERRASER" instead of the aforementioned path.

On Mar 14, 2017 9:18 AM, "Mooers, Blaine H.M. (HSC)" <Blaine-Mooers at ouhsc.edu<mailto:Blaine-Mooers at ouhsc.edu>> wrote:
Dear phenixbb,

This is a question about phenix.erraser.
I had it running in March 2016, but it no longer works.
I am using phenix-dev2686.
I am also using the rosetta_src_2016.59086_bundle that was released in November 2016.
Rosetta works fine for other tasks.
I set in my bashrc file the following: export PHENIX_ROSETTA_PATH=/Users/blaine-mooers/software/rosetta_src_2016.46.59086_bundle
If I use the gui or the command line, I get an error message that suggests using a relative path to the rosetta directory.
This does not work either.
I also tried extending the path incrementally down to the directory containing the erraser binaries.

There must be some other issue.
I suspect that between March and November 2016 that there has been reorganization of the directory hierarchy in rosetta.
There is no longer a "tools" subfolder in the top directory.
The file erraser_option.py is now located  in ./rosetta_src_2016.46.59086_bundle/main/source/src/apps/public/ERRASER.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Faculty webpage<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_department-2Dof-2Dbiochemistry-2Dand-2Dmolecular-2Dbiology_faculty_blaine-2Dmooers-2Dph-2Dd-2D&d=DwMFaQ&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=YQBjdfBLYcA51fnCQxRBEOpdTFroI86efx8VnJ2SRe0&s=wEqw-dl8sdGGOVCJ4aW8asBcDVLAJSZG-huRljDv5tE&e=>   X-ray lab (LBSF)<https://urldefense.proofpoint.com/v2/url?u=http-3A__http-3A__research.ouhsc.edu_CoreFacilities_LaboratoryofBiomolecularStructureandFunction.aspx&d=DwMFaQ&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=YQBjdfBLYcA51fnCQxRBEOpdTFroI86efx8VnJ2SRe0&s=lzQxmPaN9kVtECclHRoiV_12-D8lhJjTZwmi5KTb5vg&e=>   Molecular Graphics<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.oumedicine.com_docs_default-2Dsource_ad-2Dbiochemistry-2Dworkfiles_moleculargraphicslinks.html&d=DwMFaQ&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=YQBjdfBLYcA51fnCQxRBEOpdTFroI86efx8VnJ2SRe0&s=2bTqP60B7-C-Tw5Xd7Cae5wKcxovO6HSLxQKi2OfGAE&e=> Links <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.oumedicine.com_docs_default-2Dsource_ad-2Dbiochemistry-2Dworkfiles_MolecularGraphicsLinks.html&d=DwMFaQ&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=YQBjdfBLYcA51fnCQxRBEOpdTFroI86efx8VnJ2SRe0&s=3LUkxFa6m2ASL5-tmg_nzs9O4ubuA9z9fY7Wo5Ftp8g&e=>  Small Angle Scattering <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_docs_default-2Dsource_ad-2Dbiochemistry-2Dworkfiles_small-2Dangle-2Dscattering-2Dlinks-2D27aug2014.html-3Fsfvrsn-3D0&d=DwMFaQ&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=YQBjdfBLYcA51fnCQxRBEOpdTFroI86efx8VnJ2SRe0&s=g21Yvzkh0T3FvHHVL93etNXtCTYIOyMO74IspVSmLDA&e=>
office: (405) 271-8300<tel:(405)%20271-8300>   lab: (405) 271-8313<tel:(405)%20271-8313>   e-mail:  blaine-mooers at ouhsc.edu<mailto:blaine-mooers at ouhsc.edu>

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