However, when I tried my data, I always got

"terminate called after throwing an instance of 'std::bad_alloc'"

Google suggests maybe memory is not enough.

I used VirutalBox and assign 8gb memory to it.

My protein has ~3000 residues. I guess this will use more memory but how much RAM I need?

Or the error is due to some other problem?

Thank for any inputs.

Lee

------------------------------

Message: 3
Date: Tue, 05 Nov 2013 14:26:00 +0100
From: Jan Gebauer <[email protected]>
To: PHENIX user mailing list <[email protected]>
Subject: Re: [phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS
Message-ID: <[email protected]>
Content-Type: text/plain; charset="utf-8"

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