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Don't know how to extract scores from a RNA de novo silent file.

Submitted by Basantab on Wed, 2011-11-23 17:27

Hi,

I have a silent file containing the structures from a RNA de novo run. I have been able to extract the pdbs using the rna_extract application, but I'm unable to extract scorefiles, no matter what flags I use, it just extracts the PDB files with no scores in them. I would like to know which is the right application/flag to use, or if there's any simple console command to get the structures in an order according to increasing total energy.

So far I have tried:
rna_extract.exe -out:file:scores_only -database ./rosetta_database -in:file:silent myfile.silent

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Rosetta 3 - Applications

Comparative Modeling databases?

Submitted by nitroamos on Wed, 2011-11-23 14:54

Hello --

I'm interested in digging deeper into what was presented in this paper:

Incorporation of evolutionary information into Rosetta comparative modeling
James Thompson1,*, David Baker1,2,3
Proteins: Structure, Function, and Bioinformatics
Volume 79, Issue 8, pages 2380–2388, August 2011
http://onlinelibrary.wiley.com/doi/10.1002/prot.23046/abstract

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Rosetta 3 - General

rosetta scores for mutated structures

Submitted by harshkhare on Wed, 2011-11-23 09:30

Hello,
I have written a script for mutating a particular residue to all 20 residue types and scoring all the 20 mutated structures. I am not able to understand how exactly the scoring is done, as some mutations have given unexpected scores.
Following are the lines in command line output. The original residue was LEU at position 27. If you compare the scores of LEU-LEU mutation(score = -4.0111e-07) and LEU-ILE mutation(score = 25.2522), the LEU-ILE score is unexpectedly high.

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Rosetta 3 - Applications

Modelling a loopless structure

Submitted by jhbrown on Tue, 2011-11-22 11:39

I am new to Rosetta, and I would like to have Rosetta3.3 predict the detailed structure of a sequence homologous to that of a short two-chain loopless structure (it is an alpha-helical coiled coil). I tried comparative modeling in minirosetta, and since there are no loops, I simply tried deleting all the -loops commands, but the program was coming back with an error: Fragment IO: could not open file frag9. Do I have to supply fragment files and loop commands when there are no loops? And how would I do that? Thanks for any help.

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Rosetta 3 - General

Rosetta 3.3 installation warnings

Submitted by jjlee2 on Mon, 2011-11-21 09:19

I am trying to install Rosetta 3.3 on a cluster, but every time I try to install it, I get a ton of warnings (but no actual errors). I was wondering if these warnings are something I should worry about and, if so, how I should fix them. Some examples of the warnings are below and I have attached the whole error file.


src/protocols/toolbox/pose_metric_calculators/RotamerBoltzCalculator.cc: In mem\
ber function 'protocols::moves::MinMoverOP protocols::toolbox::pose_metric_calc\
ulators::RotamerBoltzCalculator::init_minmover(core::pose::Pose&, core::Size, b\

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Rosetta 3 - Build/Install

Hbond tripped

Submitted by alejandro on Mon, 2011-11-21 04:17

Good morning everybody,

I use Rosetta as part of a Monte Carlo algorithm. The main operations Rosetta performs are :
1) the scoring of a pose;
2) the modification of the pose (using modifications of the psi and phi angles, RigidBodyTransMovers and RigidBodySpinMovers).

It works quite well on average but sometimes, without any apparent reason, Rosetta crashes because of a "HBond tripped".

Can anybody help with that?

1) What does exactly this error mean?
2) Where does it come from (scoring functions or movers)?
3) Is it normal to get such an error ?
4) How do I get rid of it?

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Rosetta 3 - General

cluster.mpi running in MPI mode?

Submitted by sacch on Fri, 2011-11-18 23:30

Hi all,

I am aware that the application cluster does produce mpi version when rosetta is compiled in mpi mode. When I look into the output clog file in the folder, it seems all threads are doing identical procedures. I am wondering if it really used MPI to accelerate the calculation? Or is it just many threads doing the same job in the same time?

Thanks~

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Rosetta 3 - Applications

How to score the crystal structure?

Submitted by vsjasion on Fri, 2011-11-18 15:49

Hi All,

I have a control system in which the co-crystal structure is determined. I would like to have rosetta only score the input pdb without docking, so that I can compare the crystal coordinates with the results. I would also like to be able to score the prepacked structure used for the actual studies.

I used the flag -run:score_only and this worked, but there was a score.sc file and a pdb file. Also, the rms was 30 in the score file. I re-ran and sure enough, the score was different, indicating that it is actually docking not merely scoring.

The flags I used were:

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Rosetta 3 - General

loop modeling during enzyme design?

Submitted by lzx32 on Wed, 2011-11-16 00:30

Dear developers:

I noticed that some loop modeling options (e.g. kic_looop_sampling) are now included for the enzyme_design.linuxgccrelease protocol in Rosetta3.3.

It seems that the capacity to remodel loops in the substrate-binding pocket will significantly improve the enzyme_design protocol. But since this has not been mentioned in any papers or tutorials, are the loop modeling options fully working now, or are they still under development?

Thanks for reading...

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