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Holes output interpretation

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

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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Questions about Monte Carlo Simulated Annealing algorithm in the design protocols

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

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

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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How to get multiple chains in PDB from Fold and Dock

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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Question regarding Mlipo score

Dear all,

wanting to use the membrane abinitio application, I'd really like to know how the "Mlipo" score is calculated. I assume also using the .lips4 file as input? And is the .lips4 file used for anything else? I could not find this piece of information in the manual/forum and also not in the paper describing the membrane low-res. application (Proteins 2006, 62:1010).

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how to pick fragments for a transmembrane protein

Dear all,

I have created fragments with make_frags.pl script using the following command lne:
make_fragments.pl -verbose -nosam -nopsipred -nojufo -samfile UapA_SAM.ss2 -id UapA_ UapA.fasta

where UapA_SAM.ss2 is the SAM-predicted secondary structure in pripred_ss2 format, created in the following way:
ss_pred_converter.py --sam UapA.rdb > UapA_SAM.ss2

The UapA.rdb file has been obtained from ROBETTA server. Is this OK?

The default weight file used for fragment picking by "make_fragments.pl" script is the following:
# score name priority wght min_allowed extras

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