[phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS

Tue Nov 5 05:26:00 PST 2013

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 <tel:+64%209%203737599;84607>
>
> On 1/11/2013, at 8:30 PM, Jan Gebauer <jan.gebauer at uni-koeln.de
> <mailto: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/
>>>>
>>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org <mailto: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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