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what is "-relax:sequence" ?

Submitted by Anonymous on Fri, 2012-06-08 06:31

in the user guide for "how to prepare structures for use in Rosetta", Steven C. recommended to use -relax:sequence. What is this parameter? It seems relax manual only mentions -relax:fast -relax:thorough, and the deprecated -relax:classic.

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two questions about "Prepare structures for use in Rosetta"

Submitted by Anonymous on Wed, 2012-06-06 08:13

I use Rosetta 3.4 on Ubuntu 12.04 64bit.

* Question 1: Positive total_energy after relax with all-heavy-atom constraints?
I have a NMR structure model which I want to "prepare" for rosetta using relax with all-heavy-atom constraints.
Following the "short protocol" given at:
http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/dd/d...

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Where is the RosettaHoles2 executable?

Submitted by lah435 on Mon, 2012-06-04 15:15

What is the difference between the following executables?
Do any of them correspond to RosettaHoles2?
holes.macgccrelease holes_daball_input.macgccrelease packstat.macgccrelease pack_stat_energy.macgccrelease
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Thanks to whoever knows the answer.

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Holes output interpretation

Submitted by lah435 on Mon, 2012-06-04 15:02

I have finally run Rosetta Holes successfully, however since there is no documentation of any kind for Holes, I don't know how to interpret the output:
RosettaHoles: HEADER File/Tag RosHol resl dec25 dec15 AAresl AAdec25 AAdec15 RosScore RosettaHoles: RMS 1UBQ.pdb 1.7825 1.7813 -1.9173 -0.6209 1072.32 -1154.23 -373.78 -16.036 0.0000

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Help with pyRosetta python scripting for protein manipulation

Submitted by pepfolder on Thu, 2012-05-31 14:01

We have recently begun learning to use pyRosetta. We have been using Foldit (both standalone and the online game version) for a while to do some protein modelling. The online version of Foldit has easy to use Lua scripts that make protein manipulation very easy but we can't export the pdb files. We would like to be able to do similar scripting in pyRosetta that we can do in Lua. Does anyone have information on how the Foldit Lua script commands translate to equivalent functions in pyRosetta? For example, what is the equivalent of foldit's rubber-bands in pyRosetta?

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PyRosetta - General

Questions about Monte Carlo Simulated Annealing algorithm in the design protocols

Submitted by mdyini on Thu, 2012-05-31 12:39

Dear all,

When I am using the design protocols (mostly fixbb design), I'm always wondering how much of the sequence space was effectively searched by the Monte Carlo Simulated Annealing method. For example, in a fixbb design at 13 positions, the output log file said there were totaly 15459 rotamers, and I generated 1000 decoys. So there should be 1000 sampling trajectories of random substitutions from the 15459 rotamers, right? In this case, I noticed the resulting sequences were pretty converged. My questions are:

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a question about ligand docking

Submitted by yzhou on Wed, 2012-05-30 18:57

Hi,I am a brand new user in using Rosetta.
In my case, I want to dock a ligand to a protein with the protein conformation fixed.
I have tried default protocol of ligand_docking but it did not work.
The conformation of some side chains changed.
So, does someone have the idea of designing a proper protocol to achieve this goal?
Thanks in advance.

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problems installing Rosetta on ubuntu11.10

Submitted by cuiyoutian on Tue, 2012-05-29 23:42

dear friends, I am going to install rosetta3.4 in Ubuntu11.10,gcc4.6.1,python2.7.2.
I come across such errors:
scons: *** [build/src/release/linux/3.0/32/x86/gcc/4.6/libObjexxFCL.so] UnicodeDecodeError : 'ascii' codec can't decode byte 0xe4 in position 91: ordinal not in range(128).
could U help me?

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Rosetta 3 - Build/Install

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How to get multiple chains in PDB from Fold and Dock

Submitted by arthuc01 on Tue, 2012-05-29 02:05

I have attempted to run fold and dock on a protein (see an alternate post on this board for details) with C4 symmetry defined but but when I run:

/home/chxcja/rosetta3.3_bundles/rosetta_source/bin/score.linuxgccrelease -database ~/rosetta3.3_bundles/rosetta_database/ -in:file:silent default-c4membrane.out -in::file::fullatom -out:output

to get a pdb file of the models the pdbs only contain 1 chain.

Does anyone have any ideas how I can get the pdb of the complex (in this case a C4 symmetric structure).

Thanks for your help

Chris

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