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

Wed Mar 15 17:10:31 PDT 2017

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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Mar 14, 2017 at 11:23 AM, Mooers, Blaine H.M. (HSC) <
Blaine-Mooers at ouhsc.edu> 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/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> 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:
> blaine-mooers at ouhsc.edu
>
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