[phenixbb] Setting up MR_Rosetta

Morten Groftehauge mortengroftehauge.work at gmail.com
Thu Nov 8 05:21:39 PST 2012


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 <georg.mlynek at univie.ac.at> wrote:

>  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 link<https://www.dropbox.com/s/207t7hdqt0vbvp7/Screen%20shot%202012-11-02%20at%208.58.47%20AM.png>).
> 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%208.03.06%20PM.png>
> )
>
>  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 listphenixbb at phenix-online.orghttp://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: georg.mlynek at univie.ac.at
> mobil: +43 660 42 195 07
> office: +43-1-4277-52263
>
>
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>
>


-- 
Morten K Grøftehauge, PhD
Pohl Group
Durham University
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