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getting Rosetta to work with Phenix

Submitted by satyshur on Sun, 2012-03-04 12:54

I am trying to get Rosetta to work with Phenix phenix-1.7.3-928. But first I need to
get rosetta compiled. It does not compile without an error.I start with:

[rosetta@paprika ~/Desktop]$ python -V
Python 2.6.6

python scons.py bin mode=release

and it runs for a while and then:

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Rosetta 3 - Build/Install

is it possible to generate models without hydrogen?

Submitted by albumns on Fri, 2012-03-02 12:24

I am using the kinetic loop refinement protocol these days. Since my protein is large than 300aa and the loop is over 20 aa. So it is really time comsuming even I use 24 CPU to run the jobs. It only generate 1 model after one hour.... I am planning to generate 5000 loop models. Is it possible to generate the loop model with hydrogen? At least without hydrogen for the no loop region?

THX

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Rosetta 3 - General

a question about loop refinement

Submitted by albumns on Fri, 2012-03-02 09:38

Hello:
I've got a crystal structure and there is a loop region which contains 20 aa was missed. I am planning to fill in such loop by Rosetta. However, I found that there are three different methods for loop refinement in Roseeta:

Loop Modeling
Fragments Based Loop Modeling
Kinematic Loop Modeling

Do you have any idea which one is better for my case?I've complied Rosetta by command:

scons bin mode=release extra=mpi

I don't whether those refinement can be supported by mpi multiple thread.

Thank you very much
best

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Rosetta 3 - General

FloppyTail bugs for N-terminal tails

Submitted by Dave C on Thu, 2012-03-01 13:06

Hi all. Recently I've been using the FloppyTail application to try and model the N-terminal floppy region of my protein. I ran into (and solved) two issues, one that I'm sure is a genuine bug, and another that may be known but is nonetheless very serious. I am running rosetta 3.3 on a machine running MacOS server 10.5. All tests used the '-C_root' option, and had my protein listed first in the pdb.

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Rosetta 3 - Applications

ddG Monomer Low Res Protocol Convergence

Submitted by harshkhare on Thu, 2012-03-01 00:45

Dear Developers,

First question!! :-

I am using DDG Monomer to calculate ddgs for some mutants. Following the paper Kellogg-2011 I use both the Row3 (Low Resolution) and Row16 (High Resolution) protocols.

Also as is recommended in the manual page for ddg monomer (http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/d3/d...) I iterate 50 times for both protocols.

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Rosetta 3 - Applications

rosetta 3.3 compile error

Submitted by xtalqin on Wed, 2012-02-29 23:25

I have two computers； the old one compiled well and the program ran well.but the new one I tried everything
and could not compile correctly.
the error line mostly like this:

/tmp/cc9VrS4H.s: Assembler messages:
/tmp/cc9VrS4H.s:31770: Error: unknown pseudo-op: `.uleb128'
scons: *** [build/src/release/linux/2.6/64/x86/gcc/protocols/toolbox/pose_metric_calculators/DecomposeAndReweightEnergiesCalculator.os] Error 1
scons: building terminated because of errors.

I have tried Ubuntu 10.10, 11.10; fedora 14, 15
gcc 4.4 4.5 4.6
change the finline-limit to 200

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Rosetta 3 - Build/Install

fragment_picker bug

Submitted by David Hoover on Wed, 2012-02-29 11:43

The fragment_picker executable barfs on carriage returns. Can something be done about this? I've added the following line to the make_fragments.pl script:

die "$file is a dos file, yuck! Get rid of carriage returns (\\r) or run dos2unix immediately!\n" if (m/\r/);

in the loop where the SEQFILE is read.

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Rosetta 3 - Applications

RNA docking

Submitted by eschulz on Tue, 2012-02-28 03:04

Dear all,

I successfully tried protein_protein docking in PyRosetta before, but now I am trying to dock a RNA into a protein using the PyRosetta, which unfortunately fails ...

To run the docking I used the dna_dock.py script provided. When I run the script it finishes with following error message:

ERROR: unrecognized aa Ur
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 629
Traceback (most recent call last):
File "rna_dock.py", line 6, in
pose_from_pdb(p, "rnadock.pdb")
RuntimeError: unidentifiable C++ exception

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PyRosetta - General

how to run my openmp programe in rosetta3.3?

Submitted by lihowe on Mon, 2012-02-27 23:43

hello
sorry to occupy your time.
I have run my openmp program in rosetta3.0.
such as add "fopenmp" into source/tools/build/basic.setting file.
and add "gomp" in apps.src.setting file,
but while I do the same thing in rosetta3.3,
I successfully compiled but my program still run in one thread.
so now I'm not sure the above change is right or wrong?
thanks for your help!

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