Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH; problem fixed.
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 webpagehttp://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/f... X-ray lab (LBSF)http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStru... Molecular Graphicshttps://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/mol... Links https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/Mol... Small Angle Scattering http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/smal...
office: (405) 271-8300 lab: (405) 271-8313 e-mail: [email protected]
________________________________
From: Andy Watkins [[email protected]]
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 Phenix currently supports Rosetta 3.7 but this information will be used when we migrate to 3.8 support. Thanks Andy. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Mar 14, 2017 at 11:23 AM, Mooers, Blaine H.M. (HSC) < [email protected]> wrote:
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/f... X-ray lab (LBSF) http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStru... Molecular Graphics https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/mol... Links https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/Mol... Small Angle Scattering http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/smal... office: (405) 271-8300 lab: (405) 271-8313 e-mail: [email protected] ------------------------------ *From:* Andy Watkins [[email protected]] *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)" < [email protected]> 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 lab: (405) 271-8313 e-mail: [email protected]
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participants (2)
-
Mooers, Blaine H.M. (HSC) -
Nigel Moriarty