Hi, I'm testing Rosetta 3.2+PHENIX 1.7-650, and in the phenix.mr_rosetta output, I see: Checking rosetta paths: rosetta binary: /programs/l/rosetta/3.2/rosetta_source/bin/mr_protocols.default database_dir: /programs/l/rosetta/3.2/rosetta_database script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/public/electron_density pilot_script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/pilot/frank/ In the script directory, the C++ files were not built along with the regular Rosetta build. Do those need to be compiled for the target platform? Also, the pilot_script_dir is empty. Is there supposed to be something in there? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Hi Ben, All you should need is the /programs/l/rosetta/3.2/rosetta_source/bin/mr_protocols.default and the /programs/l/rosetta/3.2/rosetta_database If you set "align_with_sculptor=False" you would also need the (missing) files in pilot_script_dir. (I didn't realize these files are not in the rosetta distribution.) Let me know of problems. Note: it may be helpful to run one or more of the regression tests on this to make sure you have everything set up correctly. You can do this for example with one of these: phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up # 10 sec, quick test for installation phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta # one full test, takes 15 minutes phenix_regression.wizards.test_command_line_rosetta_quick_tests # 34 tests, takes an hour All the best, Tom T On Jan 31, 2011, at 1:15 PM, Ben Eisenbraun wrote:
Hi,
I'm testing Rosetta 3.2+PHENIX 1.7-650, and in the phenix.mr_rosetta output, I see:
Checking rosetta paths: rosetta binary: /programs/l/rosetta/3.2/rosetta_source/bin/mr_protocols.default database_dir: /programs/l/rosetta/3.2/rosetta_database script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/public/electron_density pilot_script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/pilot/frank/
In the script directory, the C++ files were not built along with the regular Rosetta build. Do those need to be compiled for the target platform?
Also, the pilot_script_dir is empty. Is there supposed to be something in there?
Thanks.
-ben
-- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Hi Tom,
All you should need is the...
Great. Thanks.
Note: it may be helpful to run one or more of the regression tests on this to make sure you have everything set up correctly. You can do this for example with one of these:
phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta # one full test, takes 15 minutes
I saw the note about the regression test in the docs a few minutes after I sent the last email, and it passed the default 7 tests without issue. (As an side, the whole list of phenix_regression.foo tools looks kind of exciting. That tells you something about my personality I guess. I'm not sure what. :-) The docs here need a little attention: http://www.phenix-online.org/documentation/mr_rosetta.htm Some of the blocks of code lead with an incorrect: phenix.mr_rosetta exptl_fobs_phases_freeR_flags.mtz sequence.dat And Rosetta 3.2 is out now, so that part can be updated. Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Hi Ben, Thanks, yes, I fixed the typos in the mr_rosetta documentation last week and updated with Rosetta 3.2... but 1 day too late for the 1.7 release. So it will be in nightly builds that are currently available. I like having the phenix_regression tests too. It allows us to make changes from our end with so much more confidence that everything is going to work. All the best, Tom T
Hi Tom,
All you should need is the...
Great. Thanks.
Note: it may be helpful to run one or more of the regression tests on this to make sure you have everything set up correctly. You can do this for example with one of these:
phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta # one full test, takes 15 minutes
I saw the note about the regression test in the docs a few minutes after I sent the last email, and it passed the default 7 tests without issue.
(As an side, the whole list of phenix_regression.foo tools looks kind of exciting. That tells you something about my personality I guess. I'm not sure what. :-)
The docs here need a little attention:
http://www.phenix-online.org/documentation/mr_rosetta.htm
Some of the blocks of code lead with an incorrect:
phenix.mr_rosetta exptl_fobs_phases_freeR_flags.mtz sequence.dat
And Rosetta 3.2 is out now, so that part can be updated.
Thanks.
-ben
-- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi again Ben, I forgot to mention that there are also several worked-out examples for phenix.mr_rosetta: 1. If you go to: $PHENIX/phenix_examples/HNP3-mr-rosetta there is a demo example for a small structure. 2. If you go to: http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/ you will find several real examples with scripts in the blind_tests/ directory. All the best, Tom T On Jan 31, 2011, at 1:15 PM, Ben Eisenbraun wrote:
Hi,
I'm testing Rosetta 3.2+PHENIX 1.7-650, and in the phenix.mr_rosetta output, I see:
Checking rosetta paths: rosetta binary: /programs/l/rosetta/3.2/rosetta_source/bin/mr_protocols.default database_dir: /programs/l/rosetta/3.2/rosetta_database script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/public/electron_density pilot_script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/pilot/frank/
In the script directory, the C++ files were not built along with the regular Rosetta build. Do those need to be compiled for the target platform?
Also, the pilot_script_dir is empty. Is there supposed to be something in there?
Thanks.
-ben
-- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
participants (3)
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Ben Eisenbraun -
Thomas C. Terwilliger -
Tom Terwilliger