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Cannot create cst files from upl files

Submitted by road runner on Wed, 2015-11-11 22:07
Category: 
Constraints

Hi,

I am trying to do structure calculations with CS-Rosetta/Rasrec. Test data from the Rosetta Toolbox work perfectly fine, but my own data make trouble: I am not able to set up a run with NOE data. The .upl files were already trimmed corresponding to trimming the termini as well as renumbered, but converting the cyana .upl files into rosetta .cst files fails, since "there is not enough information to determine the offset". It looks like the sequence information from the upl files cannot be matched with the fasta sequence.

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Rosetta 3 - General

RosettaLigand: How to score native pose in protein-ligand docking experiment?

Submitted by Ryhon Wang on Tue, 2015-11-10 01:30
Category: 
Docking

Hi Everyone:
I'm working on protein-ligand docking experiment. I have an odd problem concerning how to calculate the "native pose" total_score , interface_delta and ligand_auto_rms_no_super value from rosettaligand docking experiment.

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Rosetta 3 - Applications

Protein/Protein Ddg demo: How to write predicted mutant structures?

Submitted by cossio on Wed, 2015-11-04 20:14
Category: 
Structure prediction
Design

I am following the protein/protein Ddg demo:

https://www.rosettacommons.org/demos/latest/public/calculate_protein_protein_ddg/README

I am wondering if there is a way to modify the script mutation_script.xml so that I can write the predicted structures of the mutants to PDB files?

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Rosetta 3 - Applications

What is "repack", "prepack"?

Submitted by cossio on Wed, 2015-11-04 17:59
Category: 
Structure prediction
Docking
Design

All over the place in Rosetta Documentation, I find the terms "repack", "prepack". But I have not found their definitions. I suspect that "repack" and "prepack" refer to conformational samplings where only amino acid side chains are moved, while the backbone remains fixed, but I can't be sure. Is it in this sense that these terms are used here?

What are the definitions of "repack" and "prepack" (in the common usage of these terms in the ROSETTA community)?

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Rosetta 3 - General

FloppyTail :How to specify range of design(mutation)

Submitted by syoifczeri on Mon, 2015-11-02 04:14
Category: 
Structure prediction

Hello 

 

I am working with Floppy tail.

I am planning to do Floppytail with the amino acid design in specified range (250 to 255 in Rosetta count at chain B protein).

Is that possible to specify the design range by resfile like below? 

I couldn't fully understand packer task control......

 

## inside of resfile##

250 B ALLAA

251 B ALLAA

252 B ALLAA

253 B ALLAA

254 B ALLAA

255 B ALLAA

 

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Rosetta 3 - Applications

How does Rosetta select atom pairs for Lennard Jones Potential calculations?

Submitted by bowang2013 on Thu, 2015-10-29 08:04
Category: 
Scoring

Hi,

I am a new user for Rosetta and I am now trying to figure out how exactly PyRosetta is making the atom pair selection for scoring function calculations in general. For example, when we calculate pair-potential we will not include those bonded atom pairs and we also do not consider those who are two chemical bonds away. I wonder what is the selection rule for Rosetta? And where I could find the source code in the Rosetta folder?

 

Many thanks.

 

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PyRosetta - General

JD2 MPI

Submitted by jrcf on Wed, 2015-10-28 14:45
Category: 
Structure prediction

Hello

Guys, I'm working with ab initio, homology modeling and docking. I realized running abinitio and modeling by homology the MPI automatically chooses how it will be run the job. The problem is that the abinitio is running easy, but the homology modeling running on the server is so slow as running on my pc simple laboratory by analyzing the output files realized that the homology modeling is used this Procolo (protocols.jd2. MPIFileBufJobDistributor), and abinitio (protocols.jobdist.JobDistributors) which is efficient in my view.

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Rosetta 3 - Applications

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