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Rosetta scoring

Submitted by Dimitrov on Thu, 2012-09-20 01:54

Hi,
I am a newbie in working with Rosetta. I used a flexpeptdock protocol to dock a peptide into protein. I tried to use scoring protocol and extract information from a silent file (result from docking) with 100 poses. After running "score.linuxgccrelease" with the default commands, rosetta starts and freeze with:
protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1
Before I started Rosetta I compiled it with the mpi option. Is it possible this to be the reason for freezing?
Thanks.

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Loop Modeling Deletes Residues

Submitted by Julix on Wed, 2012-09-05 10:14

Hello everybody,

I want to model some loops and the n-terminus of a protein.

The n-terminus is 45 residues long and I know the positions of the residues 14-20.
So I have created a homology model of my protein with these residues in correct position and now want to use Rosetta to improve the loops and the n-terminus before and after these 6 residues that I know.

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Comparative modeling stops with "no more batches to process... " / no output

Submitted by eskici on Tue, 2012-08-28 12:13

I have been trying to built a model using Rosetta 3.4 but it fails with "no more batches to process... ". No output is produced or any other errors (Except a warning about missing OXT residue at the termini). I have attached the log file, part of the .aln file and the flag file that I have been using.

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protein design question

Submitted by bo on Fri, 2012-08-24 10:41

Hey all, I've two questions, which I didn't found relevant post in the forum.

1. One of my protein has selenocysteine residues in it. How can I deal with it? I don't want to simply remove it since it's near to the active site. I assume I can just replace the atom name "SE" in the pdb with "S" and change "HETATM" to "ATM", but Se and S aren't the same size, which may cause different bond length?

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KeyError: "Unknown version number 4.7 for compiler 'gcc'" on Fedora 17

Submitted by tevang on Thu, 2012-08-23 06:21

Greetings,

I am trying to compile Rosetta 3.4 on Fedora 17 but I get the following error:

$ python scons.py bin mode=release
scons: Reading SConscript files ...
Traceback (most recent call last):
File "/home/thomas/Programs/Rosetta3.4/rosetta_source/SConstruct", line 141, in main
build = SConscript("tools/build/setup.py")
File "/home/thomas/Programs/Rosetta3.4/rosetta_source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614, in __call__
return method(*args, **kw)

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Rosetta 3 - Build/Install

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Copying angles (pose.set_phi()) from a substructure with the same sequence to pose doesn't produce the exact same substructure?

Submitted by resiros on Wed, 2012-08-22 07:20

Dear Rosetta Gurus,

I'm writing an extension to the Abinitio Protocol, the code I will be describing is called exactly after setup_fold() in AbrelaxApplication. Now let me describe the input and what I'm trying to do:

I use as input two poses, let's call them "model" and "prediction", both are sequencially identical.
"prediction" is the extended pose created in AbrelaxApplication::setup_fold(), "model" is a pose my class loads exterally from a pdb file of an idealized protein in a Centroid fashion.

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relax constraints not minimized

Submitted by m_grisewood on Fri, 2012-08-10 08:31

To whomever this may concern,

I am trying to run relax with constraints. The constraints are read in, and I verified by hand that the values within the score output file are accurate. However, the relaxation does not seem to move the atoms to reduce the constraint score. The command I am using is relax.linuxgccrelease @inputs.inp, where inputs.inp contains the following text:

-database /gpfs/group/cdm/rosetta/3.4/rosetta_database/
-in:file:s my_file.pdb
-out:overwrite
-cst_fa_file constraints.cst
-cst_file constraints.cst
-cst_fa_weight 1.0

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Trouble building PyRosetta on Linux Mint 13 (Maya) 64-bit / Ubuntu 12.04 (Precise Pangolin)

Submitted by ShaneOConnor on Fri, 2012-06-29 14:44

Hi mini,

I had a little trouble building PyRosetta r46030 64-bit on Linux Mint 13 (Maya) 64-bit. This revision corresponds to PyRosetta v2.011. The problems were easy to fix but since they are currently undocumented*, I thought I would list the problems and solutions here. The main problem I had seems specific to Python 2.6 and certain Ubuntu/Mint distributions so it is no surprise that it is not in the documentation. I include all the steps I took for completeness and add some comments for those new to Linux.

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PyRosetta - Build/Install

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Discarding atoms for fixbb

Submitted by Jacob-kong on Tue, 2012-06-26 06:23

Hi everyone,

When i use the fixbb executable under the directory of /integration/test/fixbb, Rosetta always output the following warning messages,such as:

core.io.pdb.file_data: [ WARNING ] discarding 7 atoms at position 1 in file 1l2y.pdb. Best match rsd_type: ASN_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 2 in file 1l2y.pdb. Best match rsd_type: LEU
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 3 in file 1l2y.pdb. Best match rsd_type: TYR

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