October 2017 - phenixbb - phenix-online.org

Rosetta installation
by Daniele de Sanctis 08 Oct '17

08 Oct '17

Hi all I have some trouble installing rosetta. I followed the instruction as in https://www.phenix-online.org/documentation/reference/rosetta_install.html and everything went ok up to % rosetta.build_phenix_interface nproc=n but then % rosetta.run_tests fails with Rosetta command-line arguments: -parser:protocol /buffer/desancti/xtal/rosetta_src_2016.32.58837_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 1yjp_rosetta_in.pdb -mtzfile 1yjp_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1yjp_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -score:weights talaris2013_cart -nstruct 1 Generating 2 models on 1 processors... DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) Traceback (most recent call last): File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module> run(sys.argv[1:], create_dir=True) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Any idea? thanks Daniele

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Running Phaser with a already placed solution from a previous job
by vincent Chaptal 05 Oct '17

05 Oct '17

Dear everyone, this sounds trivial but I somehow can't make it work so I would appreciate any pointer. I have placed a component using phaser and would like to expand my search using this already placed component as partial solution. I open the full-featured interface of phaser in the GUI and select the box "Use partial solution from previous job" and select the job (nothing seems to happen there). I define my ensembles with ensemble_1 as "fixed partial solution" and ensemble_2 the one to search for. I then get the error message that "ense_1 from previous job is not specified on the current ensemble tab". Using the info button I see that "It is best to do this by modifying the configuration of the GUI from the previous Phaser run instead of starting from scratch, because the stored solutions do not contain the definitions of the search ensembles" but I don't understand what is asked for me to do here. When I restore the previous job, I can't see how I can start a new search from there. Any help would be greatly appreciated. Thanks Vincent I'm using phenix 1.12-2829. -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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map model correlations in real_space_refine
by Daniel Larsson 04 Oct '17

04 Oct '17

In version 1.12, what does the new map correlation numbers CC_mask, CC_volume and CC_peak in the log mean? How do they relate to the old "Map CC (whole unit cell)" and "Map CC (around atoms)" values (which in my opinion are more intuitive/descriptive and very useful numbers and I don't understand why they are no longer written to the log). Regards, Daniel

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