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

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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What is "repack", "prepack"?

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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pose.replace_residue() & incorrect scoring

Category: 
Design
Scoring

Hi developers,

I wasn't sure where to submit bug reports so I'm posting here instead.

I've noticed a scoring error after repeated pose.replace_residue() function calls. The final pose after repeated calls to replace_residue() ends up having a score substantially lower (often < -50 Rosetta energy units) than when scored using the scoring application or if the pose is loaded upon application initialization.

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fixbb algorithm reference?

Category: 
Design

Hi,

I'm interested in understanding how the fixbb application works. It mentions in the documentation page:

https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d4/d68/fixbb.html

a stochastic simulated annealing approach is used. However, I do not see a description of this approach in the references on that page.

I did find a reference to a Metropolis Monte Carol procedure here:

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ERROR: Rosetta does not recognize the property: SIDECHAIN_THIOL, when running minimize_with_cst.linuxgccrelease

Category: 
Design

This is the command I am trying to execute (taken from here: https://www.rosettacommons.org/docs/latest/application_documentation/ana..., in the Preminimization of the Input Structures paragraph, in High Resolution Protocol):

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loop modeling

Category: 
Design

Hi,

I am trying to mutate the residues of a loop using resfile but it seems that the rosetta doesn't read the resfile at all. I checked this by adding a random sentence and ran the job, which ran perfectly but with native loop sequence. Here are the options which I used for loop modeling:

flag file:

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score:weights for fixbb application in Rosetta 3.5

Category: 
Design

Hi,

If you specify a weights file using the option '-score:weights' , will that weighted scoring function be used in optimizing side chain placement? That is, does the simulated annealing algorithm incorporate the scoring function specified by '-score:weights', or is 'score:weights' only used in the final scoring of the structure AFTER side chains are placed and the designed PDB is complete?

Thanks,
Tyler

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Output fasta of enzdes generated pdbs

Category: 
Design

Hi everyone,

I am using enzyme design application to mutate my enzyme. How can I extract a list of the pdb name, residues and residue number from the output generated by Rosetta.

The sequence recovery does something similar, but i need to know what residues have changed in what position. I am looking for trends hence I need to do this fo a bunch of pdbs that meet my cut off. Is there a quick way of getting a series of fastA files that I can view on any sequence alignment tool or a table ?

Thanks in advance for your help

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sequence_tolerance optimize the binding to chemical compounds

Category: 
Design

Dear all,

can I used sequence_tolerance to optimize the binding pocket on a protein for a chemical compounds?

I used molfile_to_params.py to generate a params file for the compound. But I do not know how to feed this to sequence_tolerance?

Thank you for the help.

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