<div dir="ltr">Blaine<div><br></div><div>Phenix currently supports Rosetta 3.7 but this information will be used when we migrate to 3.8 support.</div><div><br></div><div>Thanks Andy.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 14, 2017 at 11:23 AM, Mooers, Blaine H.M. (HSC) <span dir="ltr"><<a href="mailto:Blaine-Mooers@ouhsc.edu" target="_blank">Blaine-Mooers@ouhsc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Hi Andy,<br>
<br>
Thank you for the clarification!<br>
<br>
Yes, I was wrong. There is still a tools subdirectory at the top level.<br>
<br>
I installed the latest version of Rosetta from source.<br>
This is version 3.8, the Feb. 25th, 2017 release.<br>
The rosetta\_options.py file is in the same location: main/source/src/apps/public/<wbr>ERRASER.<br>
<br>
Following up on your suggestion, I edited the file erraser.py in<br>
/Applications/phenix-dev-2686/<wbr>modules/phenix/phenix/erraser<br>
by replacing line 543 with the following:<br>
<br>
file_path = os.path.join(params.<wbr>directories.rosetta_path, 'main/source/src/apps/public/<wbr>ERRASER')<br>
<br>
Phenix.erraser now runs. <br>
<br>
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<div class="m_7935620430895549725PlainText">Best regards,<br>
<br>
Blaine<br>
<br>
Blaine Mooers, Ph.D.<br>
Assistant Professor<br>
Department of Biochemistry and Molecular Biology, College of Medicine<br>
University of Oklahoma Health Sciences Center <br>
975 NE 10th Street, BRC 466</div>
<div class="m_7935620430895549725PlainText">Oklahoma City, OK 73104-5419<br>
</div>
<div class="m_7935620430895549725PlainText"><a href="http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-" target="_blank">Faculty webpage</a> <a href="http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStructureandFunction.aspx" target="_blank">X-ray
lab (LBSF)</a> <a href="https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/moleculargraphicslinks.html" target="_blank">Molecular Graphics</a> Links<a href="https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/MolecularGraphicsLinks.html" target="_blank"> </a>
<a href="http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0" target="_blank">
Small Angle Scattering </a><br>
office: <a href="tel:(405)%20271-8300" value="+14052718300" target="_blank">(405) 271-8300</a> lab: <a href="tel:(405)%20271-8313" value="+14052718313" target="_blank">(405) 271-8313</a> e-mail: <a href="mailto:blaine-mooers@ouhsc.edu" target="_blank">blaine-mooers@ouhsc.edu</a><br>
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<div id="m_7935620430895549725divRpF782433" style="direction:ltr"><font size="2" color="#000000" face="Tahoma"><b>From:</b> Andy Watkins [<a href="mailto:andy.watkins2@gmail.com" target="_blank">andy.watkins2@gmail.com</a>]<br>
<b>Sent:</b> Tuesday, March 14, 2017 11:53 AM<br>
<b>To:</b> Mooers, Blaine H.M. (HSC)<br>
<b>Subject:</b> Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH<br>
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<div>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.<br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mar 14, 2017 9:18 AM, "Mooers, Blaine H.M. (HSC)" <<a href="mailto:Blaine-Mooers@ouhsc.edu" target="_blank">Blaine-Mooers@ouhsc.edu</a>> wrote:<br type="attribution">
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<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Dear phenixbb,<br>
<br>
This is a question about phenix.erraser. <br>
I had it running in March 2016, but it no longer works.<br>
I am using phenix-dev2686.<br>
I am also using the rosetta_src_2016.59086_bundle that was released in November 2016.<br>
Rosetta works fine for other tasks.<br>
I set in my bashrc file the following: export PHENIX_ROSETTA_PATH=/Users/bla<wbr>ine-mooers/software/rosetta_<wbr>src_2016.46.59086_bundle<br>
If I use the gui or the command line, I get an error message that suggests using a relative path to the rosetta directory.<br>
This does not work either.<br>
I also tried extending the path incrementally down to the directory containing the erraser binaries.<br>
<br>
There must be some other issue.<br>
I suspect that between March and November 2016 that there has been reorganization of the directory hierarchy in rosetta.
<br>
There is no longer a "tools" subfolder in the top directory. <br>
The file erraser_option.py is now located in ./rosetta_src_2016.46.59086_bu<wbr>ndle/main/source/src/apps/publ<wbr>ic/ERRASER.<br>
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<div class="m_7935620430895549725m_-3396043835849943383PlainText">Best regards,<br>
<br>
Blaine<br>
<br>
Blaine Mooers, Ph.D.<br>
Assistant Professor<br>
Department of Biochemistry and Molecular Biology, College of Medicine<br>
University of Oklahoma Health Sciences Center <br>
975 NE 10th Street, BRC 466</div>
<div class="m_7935620430895549725m_-3396043835849943383PlainText">Oklahoma City, OK 73104-5419<br>
</div>
<div class="m_7935620430895549725m_-3396043835849943383PlainText"><a href="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=" target="_blank">Faculty
webpage</a> <a href="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=" target="_blank">X-ray
lab (LBSF)</a> <a href="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=" target="_blank">Molecular
Graphics</a> Links<a href="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=" target="_blank"> </a>
<a href="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=" target="_blank">
Small Angle Scattering </a><br>
office: <a href="tel:(405)%20271-8300" value="+14052718300" target="_blank">(405) 271-8300</a> lab:
<a href="tel:(405)%20271-8313" value="+14052718313" target="_blank">(405) 271-8313</a> e-mail:
<a href="mailto:blaine-mooers@ouhsc.edu" target="_blank">blaine-mooers@ouhsc.edu</a><br>
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