[phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS

Nathaniel Echols nechols at lbl.gov
Thu Oct 31 11:02:55 PDT 2013


I will fire up an Ubuntu 12.04 virtual machine and try to reproduce this,
but it's going to take a while.  If you could send me your input files
off-list, it will help to verify whether the problem is specific to Ubuntu,
or something in your data that isn't being handled properly.

thanks,
Nat


On Thu, Oct 31, 2013 at 8:48 AM, Jan Gebauer <jan.gebauer at uni-koeln.de>wrote:

>  Dear all,
>
> I'm trying to get rosetta_refine working on ubuntu 12.04 LTS.
>
> This was the (latest) way I tried it:
>
> 1) Downloaded phenix-dev-1523 binary & installed it via installer in
> /usr/local/science/phenix4rosetta/phenix-dev-1523
> 2) Downloaded rosetta 2031wk42 and extracted it in
> /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle
> 3) Inserted into phenix_env.sh
> export
> ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin
> export
> PHENIX_ROSETTA_PATH=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/
> export
> ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database
> 4) sources phenix_env.sh
> 5) build the interface via
> rosetta.build_phenix_interface nproc=4
> 6) exceute the refinement via phenix.rosetta_refine phasermodel.pdb
> data.mtz nproc=4
>
> The programm runs fine, up to the point where it should generate models
> via rosetta, it then stops and crashes.
> I have attached some logfiles
>
> Has anyone managed to run rosetta_refine on Ubuntu? Which phenix and
> rosetta versions did you use? Ist there anything wrong on my above
> mentioned build protocol?
>
> I'm thankful for any help.
>
> Regards,
> Jan Gebauer
>
>
>
> --
> Dr. Jan Gebauer
> AG Prof. Baumann
> Institut für Biochemie / Uni-Köln
> Otto-Fischer-Str. 12-14 / 50674 Köln
> Fon: +49 (221) 470 3212	
> Fax: +49 (221) 470 5066
> http://px.uni-koeln.de/
>
>
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>
>
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