[phenixbb] Setting up MR_Rosetta

Georg Mlynek georg.mlynek at univie.ac.at
Sun Nov 4 15:48:05 PST 2012


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^(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%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 list
> phenixbb at phenix-online.org
> 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: georg.mlynek at univie.ac.at
mobil: +43 660 42 195 07
office: +43-1-4277-52263

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