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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

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

ROSIE antibody modeling- discontinuity in backbone

Submitted by wagnerek on Tue, 2015-10-27 10:18
Category: 
Structure prediction

Hi, 

I submitted a job to the ROSIE antibody queue, which ran successfully, but all the result files now have a discontinuity in the backbone 2 residues before the start of CDR L2. No residues are missing. I ran it again without the H3 modeling, and the discontinuity isn't there, so it's something during the high resolution modeling that is causing a problem. Is there anything I can do to prevent this from happening? Should I use the light chain structure from the grafted model as correct, and use the heavy chains from the more rigorous protocol?

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ROSIE - General

RosettaCM Biological Assembly

Submitted by jrcf on Mon, 2015-10-26 11:01
Category: 
Structure prediction

Hi everyone,

Guys, I'm using rosettaCM, the problem is that I use a structure that is partially formed in the PDB (the rosettaCM queries the PDB to create the files) when it makes this query takes into account only part of the structure, does anyone know tell me what I change the setup_rosettaCM.py so that it takes into account the biology unit (Biological Assembly).

 

thaks

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Rosetta 3 - Applications

The following options have been set but have not yet been used

Submitted by jrcf on Fri, 2015-10-09 10:48
Category: 
Structure prediction

Hi guys...

I'm using the Basic Homology Modeling, and received this massage on the final of the execution.

protocols.jd2.JobDistributor: WARNING: The following options have been set, but have not yet been used:
        -in:file:frag3 3rvyCH1_03_05.200_v1_3
        -in:file:frag9 3rvyCH1_09_05.200_v1_3
        -in:file:psipred_ss2 3rvyCH1.ss2
        -loops:frag_files  3rvyCH1_09_05.200_v1_3 3rvyCH1_03_05.200_v1_3 none
        -out:output 
        -out:pdb 

Here is my script

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Rosetta 3 - General

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