[phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS

Tue Nov 5 05:56:10 PST 2013

This is still much too convoluted a procedure to be practical, of course.
 I promise I'll get around to looking at Ubuntu 12 this week but the VM
setup was fiasco and we're somewhat short-handed.

For what it's worth, your data ran fine on our systems, although it overfit
somewhat - I still need to try running phenix.refine as well to see if it
actually improved anything, but it's definitely an issue with the build on
your specific system.  I'll send the results separately.

-Nat

On Tue, Nov 5, 2013 at 5:26 AM, Jan Gebauer <jan.gebauer at uni-koeln.de>wrote:

>  Hi David, hi all,
>
> I now managed to at least get a test refinement working. What I mostly
> changed was the Ubuntu version.
> I have no idea why, but I managed to get it to work on Ubuntu 10.04.
>
> In principle I installed 10.04 freshly in a virtualbox and from their it
> worked rather straight-forward.
>
> Here is how I proceeded in detail for those of you who are interested:
>
> 1) Setting up a Virtualbox 4.3.2 r90405 on Ubuntu 12.04.3.
> 2) Installing the 64bit version of Ubuntu 10.04 in a virtualbox (4
> processors / 90% speed cap / 4GB Ram /VT-x enabled)
> 3) Install VBoxAdditions
> 4) Update ubuntu (sudo apt-get update)
> 5) Installing g++ and zlib library (sudo apt-get install g++ zlib1g-dev)
> 6) Installing binary version of phenix-dev-1525 to
> /usr/local/science/phenix-dev-1525 (sudo ./install
> --prefix=/usr/local/science)
> 7) Unpack rosetta_2013_wk42_bundle to
> /usr/local/science/rosetta_2013_wk42_bundle
> 8) set rossetta variables by inserting them at the start of
> /usr/local/science/pheninx-dev-1525/phenix_env.sh (just in line 3ff):
> export PHENIX_ROSETTA_PATH=/usr/local/science/rosetta_2013wk42_bundle
> export ROSETTA3_DB=/usr/local/science/rosetta_2013wk42_bundle/main/database
> export
> PATH=$PATH:/usr/local/science/rosetta_2013wk42_bundle/main/source/bin
> 9) assign ownership to active user (sudo chown gebauer:gebauer
> /usr/local/science/ -R)
> 10) Compile it (phenix.build_phenix_interface nproc=4)
> It should run without problems
>
> Testing:
> 1) Create a new directory (mkdir test && cd test)
> 2) Download testset (suggested by Nat: phenix.fetch_pdb --mtz 1yjp)
> 3) Run rosetta_refine (phenix.rosetta_refine 1yjp.pdb 1yjp.mtz nproc=4)
> In my case rFree dropped from 18.21 to 14.90. It's not a low resolution
> dataset, but it show that it general works and lowRes would potentially
> take to long for a mere testing
>
> My real data are still being processed so I have no idea how well it will
> works... only thing I found out already:
> 4.5 GB RAM for 4 processes calculating ~500Aa via rosetta seems not to be
> enough. I thereby reduced my "real run" to only one processor...
>
> Regards,
> Jan
>
>
>
>
>
>
>
>
>
>
>
> Am 01.11.2013 08:39, schrieb David Goldstone:
>
> Hi Jan,
>
>  I followed the same procedure. The only differences being that I have
> installed it to my home directory to keep it separate from our standard
> install of phenix and rosetta and I run the phenix_env.sh separately from
> the exports. I had to remove our default init.sh script from my .bashrc
> (this is our setup script for all programs ccp4 etc) and now manually
> source a different version to ensure it points to the correct version of
> phenix.
>
>  I originally had trouble with the python shared libraries but Nat has
> fixed this by building them into the binary installer.
>
>  Sorry I can't be more help
>
>  David
>
>
> ----
> Dr David Goldstone
> Senior Lecturer
> University of Auckland
> New Zealand
> Ph +64 9 3737599 x84607 <+64%209%203737599;84607>
>
> On 1/11/2013, at 8:30 PM, Jan Gebauer <jan.gebauer at uni-koeln.de> wrote:
>
>  Dear David,
>
> thanks for your remark. Indeed my paths are wrong in the mail; however,
> this is due to lazy typing... I do set the Rosetta_DB3 path corretly...
> I'm still interested to know, how you managed to install build it. Have
> you done the same procedure as described by me? (only with different
> releases?)
> Or did you do something differently?
>
> Regards,
> Jan
>
> Am Donnerstag, 31. Oktober 2013 23:11:42 schrieb David Goldstone:
>
> Dear Jan,
>
>
>  I have recently installed phenix with rosetta refine on Ubuntu 10.04
>
> using phenix-dev-1515 and rosetta_wk40_bundle.
>
>
>  This install also appears to run on an Ubuntu 12 install.
>
>
>  I think you export commands are not correct mine are as follows
>
>
>  export
>
> PHENIX_ROSETTA_PATH=/mnt/home/dgol002/programs/rosetta_2013wk40_bundle
>
> export
>
>
> ROSETTA3_DB=/mnt/home/dgol002/programs/rosetta_2013wk40_bundle/main/database
>
> export
>
>
> PATH=$PATH:/mnt/home/dgol002/programs/rosetta_2013wk40_bundle/main/source/bin
>
>
>  ie you are exporting ROSETTA_BIN twice rather than ROSETTA3_DB.
>
>
>  Hope this helps
>
>
>  David
>
>
>
>
>  On 1/11/2013 4:48 a.m., Jan Gebauer 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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>
>  phenixbb at phenix-online.org
>
>  http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>  --
>
> Dr David Goldstone
>
> Senior Lecturer & Rutherford Discovery Fellow
>
> Structural Biology
>
> University of Auckland
>
> New Zealand
>
> Ph +64 9 3737599 x84607
>
>
> --
> 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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