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rosetta 3.2.1 installation on fedora core 6

Hi,

I am getting the floowing errors after executing the "scons bin mode=release" command:-
===========================================================================================
scons: Reading SConscript files ...
svn: '.' is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/usr/local/rosetta-3.2.1/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.

Post Situation: 

Problem with HETATM entries in PDB file

Hello

I am using FARNA module for RNA denovo structure prediction. Some of the PDB files contain HETATM entries like this :

HETATM 191 P CH A 10 6.803 -7.485 -7.145 1.00 0.00 P
HETATM 192 O1P CH A 10 7.379 -8.656 -7.843 1.00 0.00 O
HETATM 193 O2P CH A 10 6.942 -6.135 -7.736 1.00 0.00 O
HETATM 194 O5* CH A 10 5.232 -7.767 -6.901 1.00 0.00 O
HETATM 195 C5* CH A 10 4.807 -8.876 -6.102 1.00 0.00 C

Post Situation: 

Questions about rosetta fragment library ranking and fragment conformation sampling algorithm

Hi, I have some questions about fragment library used for de novo folding and loop modeling.

From what I have read, the score for ranking fragment conformations in a library consists of two parts, which are from psi-blast results and secondary structure prediction results. My questions are:

1) When performing the psi-blast that contributes to the ranking of fragment conformations in a library at one position, does the psi-blast involve the whole protein sequence or just a local region around that position?

Post Situation: 

Rosetta installation

Category: 
Compilation

i am trying to install rosette latest version in ubuntu 10.10.
i have installed scons and python as minimum requirmnets.
Now how to buld rosetta...

while i am running command like :

# scons

here i am getting error.

scons bin mode=release
scons bin
scons -h
scons -H

What to do next....
can anybody help me out?

Post Situation: 

errors while running rosetta 3.1

Hi
I have two queries regarding ab initio structure prediction with cs-rosetta using rosetta-3.1:
a) For one of the runs while using the script extract_pdb3.com default.out I get the error core.io.silent: ERROR: did not find coordinates for all sequence positions for empty_tag
and only one pdb is generated. The program is still running though.

Post Situation: 

Problem with Parallel installation of Rosetta3.2

Hi ALL,

I am trying to install the parallel version of Rosetta3.2 with the command, scons bin mode=release extras=mpi
However I am getting the following error:

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
scons: Building targets ...

Post Situation: 

Remote access to Rosetta on Blue Gene or another HPC system?

Is there a parallel version of the Rosetta suite (for example, on Blue Gene) available to the general research community anywhere? My local supercomputer network (SHARCNET in Ontario, Canada) does not have Rosetta installed so I am wondering whether I can access it elsewhere? If not, are there instructions available for doing HPC installations?

Post Situation: 

Rosetta-Holes Scoring Function

I have been trying to use the scoring function to calculate the rosetta-holes score for a pdb file (Initially I am using the pdb provided in the scoring demo). I keep getting an error related to reading the input file. I think this is the input that is passed to DAlphaBall, but it might be some other problem I am unaware of. I am using the following command:

score_jd2.linuxgccrelease -s test_in.pdb -score:weights holesscore -database ../../../rosetta_database/ -holes:dalphaball "pathToDAlphaBallExe"

and I get the following error (repeated for 10 tries):

Post Situation: 

Parallel installation of Rosetta3.2 with MPI

Hi ALL,

I want to install a parallel version of Rosetta3.2 (Abinitiorelax / relax etc.) using MPI. I find some people have already done so and using it. Can someone please tell me the steps/options with which I need to install the parallel version of Rosetta3.2.
Thanks a lot in advance.

Regards,

Anirban

Post Situation: 

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