Hello guys, I am currently trying to setup MR_Rosetta but I am running into some trouble. When I run the tutorial for Defensin HNP-3 from the GUI I always get an error during the ... process (see image at this dropbox link). I know that my path for phenix and rosetta are correct since I can run the phenix_regression.wizards.test_command_line_rosetta_quick and phenix_regression.wizards.test_command_line_rosetta_quick test_rosetta_rebuild. If I try to trace down the error, I can only get the same info that I got from the GUI error message (vide supra). As additional info, here are somme details of my setup: MacBookPro 4,1 running OS 10.6.8 Core2Duo 2.5 Ghz 6 Gb RAM Rosetta 3.2 compiled with flags bin mode=release Phenix 1.8.1-1168 And my input settings for the GUI run (dropbox) Now, this might just be confusing but there was one command line test that my setup failed: phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta The error is kinda cryptic (see dropbox copy of the error) but it seem to be a discrepancy in the scoring results not a missing program or any other kind of misconfiguration. Of course, I might be wrong. Any advice? Best regards. -- Lenin Domínguez-Ramírez "And for all the current and rather silly emphasis on structural biology,understanding enzymes means understanding catalysis and catalysis is concerned with kinetics, not structure: as Jeremy Knowles aptly remarked, studying the photograph of a racehorse cannot tell you how fast it can run." Cornish-Bowden, 1995 Lenin Domínguez-Ramírez, PhD "What are we to think of an organism that loses practically all of its cellular water at ordinary temperatures and pressures and ceases to metabolize, but upon being rehydrated resumes all of the characteristics it previously exhibited?...we should be reluctant to call such an organism dead (unless we are willing to entertain the possibility of its resurrection) because it resumes an active life upon simple restoration of water."
This test error look to me like results of roundoff differences. I
Hi, I get the same error that autobuild is failing. At least you should find in MR_ROSETTA_XXXXXX/GROUP_OF_AUTOBUILD_1/RUN_1/AutoBuild_run_1_/ one finished autobuild job. In my case also on of the tests failed see below. Tom Terwilliger answered this to me: think you can ignore it. Running test_prerefine_no_data ------------------------------------------------------------ Numbers do not match: -0.08947 -0.03928 r {{ 0.86189 0.06488 -0.50292} {-0.01063 0.99387 0.11000} { 0.50698 -0.08947 0.85730}} --- r {{ 0.84507 0.05441 -0.53188} {-0.02506 0.99775 0.06225} { 0.53407 -0.03928 0.84453}} ------------------------------------------------------------ FAILED See log files test_prerefine_no_data/test_prerefine_no_data.log test_prerefine_no_data/test_prerefine_no_data_current.log ================================================================= I am running Rosetta3.4 Phenix 1.8.1-1168 Ubuntu 11.10 lenovo thinkpad w520 Intel® Core^(TM) i7-2630QM CPU @ 2.00GHz × 8 Sorry, for not helping solving the problem. Best georg. On 11/05/2012 12:13 AM, Julio Lenin wrote:
Hello guys,
I am currently trying to setup MR_Rosetta but I am running into some trouble. When I run the tutorial for Defensin HNP-3 from the GUI I always get an error during the ... process (see image at thisdropbox link https://www.dropbox.com/s/207t7hdqt0vbvp7/Screen%20shot%202012-11-02%20at%20...). I know that my path for phenix and rosetta are correct since I can run the phenix_regression.wizards.test_command_line_rosetta_quick and phenix_regression.wizards.test_command_line_rosetta_quick test_rosetta_rebuild. If I try to trace down the error, I can only get the same info that I got from the GUI error message (vide supra).
As additional info, here are somme details of my setup:
MacBookPro 4,1 running OS 10.6.8 Core2Duo 2.5 Ghz 6 Gb RAM Rosetta 3.2 compiled with flags bin mode=release Phenix 1.8.1-1168
And my input settings for the GUI run (dropbox https://www.dropbox.com/s/77jttri9cxiurms/Screen%20shot%202012-11-01%20at%20...)
Now, this might just be confusing but there was one command line test that my setup failed: phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta
The error is kinda cryptic (see dropbox copy of the error https://www.dropbox.com/s/x5kejcmsw1aejit/Test-Error.txt) but it seem to be a discrepancy in the scoring results not a missing program or any other kind of misconfiguration. Of course, I might be wrong.
Any advice?
Best regards.
-- Lenin Domínguez-Ramírez
"And for all the current and rather silly emphasis on structural biology,understanding enzymes means understanding catalysis and catalysis is concerned with kinetics, not structure: as Jeremy Knowles aptly remarked, studying the photograph of a racehorse cannot tell you how fast it can run." Cornish-Bowden, 1995
Lenin Domínguez-Ramírez, PhD
"What are we to think of an organism that loses practically all of its cellular water at ordinary temperatures and pressures and ceases to metabolize, but upon being rehydrated resumes all of the characteristics it previously exhibited?...we should be reluctant to call such an organism dead (unless we are willing to entertain the possibility of its resurrection) because it resumes an active life upon simple restoration of water."
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Mlynek Georg University of Vienna Department of Computational and Structural Biology Max F. Perutz Laboratories Campus Vienna Biocenter 5 level -2 1030 Vienna Austria e-mail: [email protected] mobil: +43 660 42 195 07 office: +43-1-4277-52263
Yeah, "autobuild has failed" after autobuild finishes (phenix 1.8.1-1160)
but I think that's supposed to be the last bit of work anyway. And it
certainly doesn't look like the right solution in my case.
Sincerely,
Morten Groftehauge
On 4 November 2012 23:48, Georg Mlynek
Hi,
I get the same error that autobuild is failing. At least you should find in MR_ROSETTA_XXXXXX/GROUP_OF_AUTOBUILD_1/RUN_1/AutoBuild_run_1_/ one finished autobuild job.
In my case also on of the tests failed see below. Tom Terwilliger answered this to me:
This test error look to me like results of roundoff differences. I think you can ignore it.
Running test_prerefine_no_data ------------------------------------------------------------ Numbers do not match: -0.08947 -0.03928 r {{ 0.86189 0.06488 -0.50292} {-0.01063 0.99387 0.11000} { 0.50698 -0.08947 0.85730}} --- r {{ 0.84507 0.05441 -0.53188} {-0.02506 0.99775 0.06225} { 0.53407 -0.03928 0.84453}} ------------------------------------------------------------ FAILED See log files test_prerefine_no_data/test_prerefine_no_data.log test_prerefine_no_data/test_prerefine_no_data_current.log =================================================================
I am running Rosetta3.4 Phenix 1.8.1-1168 Ubuntu 11.10 lenovo thinkpad w520 Intel® Core™ i7-2630QM CPU @ 2.00GHz × 8
Sorry, for not helping solving the problem.
Best georg.
On 11/05/2012 12:13 AM, Julio Lenin wrote:
Hello guys,
I am currently trying to setup MR_Rosetta but I am running into some trouble. When I run the tutorial for Defensin HNP-3 from the GUI I always get an error during the ... process (see image at this dropbox linkhttps://www.dropbox.com/s/207t7hdqt0vbvp7/Screen%20shot%202012-11-02%20at%20...). I know that my path for phenix and rosetta are correct since I can run the phenix_regression.wizards.test_command_line_rosetta_quick and phenix_regression.wizards.test_command_line_rosetta_quick test_rosetta_rebuild. If I try to trace down the error, I can only get the same info that I got from the GUI error message (vide supra).
As additional info, here are somme details of my setup:
MacBookPro 4,1 running OS 10.6.8 Core2Duo 2.5 Ghz 6 Gb RAM Rosetta 3.2 compiled with flags bin mode=release Phenix 1.8.1-1168
And my input settings for the GUI run (dropboxhttps://www.dropbox.com/s/77jttri9cxiurms/Screen%20shot%202012-11-01%20at%20... )
Now, this might just be confusing but there was one command line test that my setup failed: phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta
The error is kinda cryptic (see dropbox copy of the errorhttps://www.dropbox.com/s/x5kejcmsw1aejit/Test-Error.txt) but it seem to be a discrepancy in the scoring results not a missing program or any other kind of misconfiguration. Of course, I might be wrong.
Any advice?
Best regards.
-- Lenin Domínguez-Ramírez
"And for all the current and rather silly emphasis on structural biology,understanding enzymes means understanding catalysis and catalysis is concerned with kinetics, not structure: as Jeremy Knowles aptly remarked, studying the photograph of a racehorse cannot tell you how fast it can run." Cornish-Bowden, 1995
Lenin Domínguez-Ramírez, PhD
"What are we to think of an organism that loses practically all of its cellular water at ordinary temperatures and pressures and ceases to metabolize, but upon being rehydrated resumes all of the characteristics it previously exhibited?...we should be reluctant to call such an organism dead (unless we are willing to entertain the possibility of its resurrection) because it resumes an active life upon simple restoration of water."
_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb
-- Mlynek Georg University of Vienna Department of Computational and Structural Biology Max F. Perutz Laboratories Campus Vienna Biocenter 5 level -2 1030 Vienna Austria
e-mail: [email protected] mobil: +43 660 42 195 07 office: +43-1-4277-52263
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Morten K Grøftehauge, PhD Pohl Group Durham University
participants (3)
-
Georg Mlynek -
Julio Lenin -
Morten Groftehauge