You are here

Home

Unsolved

The problem hasn't been solved

RosettaScripts - FastRelax loops

Submitted by jtmacd on Wed, 2015-11-18 09:32
Category: 
Loop Modeling

Hi all,

I am using RosettaScripts for some loop modelling and would like to apply the FastRelax protocol to a loop region in my structure without the moves propagating down the chain.

I know that it is possible to set up a MoveMap so that only some degrees of freedom are turned on e.g.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Docking seems to not parse the -nstruct flag

Submitted by rosend on Tue, 2015-11-17 12:01
Category: 
Docking

Hello all,

I am new to Rosetta, and I am trying to get RosettaDock to work.

For the sake of simplicity, I just want to do a refinement dock, with no constraints (though I will eventually want to graduate to incorporating these).

The command I run, a modification on the example commands in Chaudhury et al. 2011:
(I did prepacking before this, with seemingly no issue.
Also, I removed the -database flag, it was causing errors and Rosetta programs seems to work without it.)

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

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.

Post Situation: 
Unsolved
Forums: 
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.

Post Situation: 
Unsolved
Forums: 
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?

Post Situation: 
Unsolved
Forums: 
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)?

Post Situation: 
Unsolved
Forums: 
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

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

what is the xxx.static.linuxgccrelease?

Submitted by syoifczeri on Sat, 2015-10-31 04:09
Category: 
Compilation

Hello

 

I have a some question.

 

I downloaded Rosetta 2015.38 source + binaries for Linux .

and I saw xxx.static.linuxgccrelease and xxx.linuxgccrelease in bin folder.

which exe is proper when I want to execute file with mpiexec command?

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Unsolved