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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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Minimization Issue: Coarse Graining to All atom modeling

Category: 
Docking
Design
Loop Modeling

Hi all,
I want to get an all atom model of my coarse grained protein structure (after adding all the side chains back). I have been using the repacking algorithm to do so, but unfortunately its not doing the job. The side chains are not packed properly. Can you help me suggesting on how to go from coarse grained protein to get an all atom model for my protein. Is there any minimization protocol that can take care of this. Kindly let me know.

Thank you.

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Pepspec options

Category: 
Design

Hi,

I'm using pepspec to design a peptide. I've been able to run the application with some options (listed below) but my peptides always seem to fly off into space, with the exception of the region near the anchor residue. I've tried a few different combinations by looking at the application documentation, but I can't seem to get anything that looks "reasonable". My options are:

-pepspec::soft_wts soft_rep.wts

-pepspec::interface_cutoff 5
-pepspec::clash_cutoff 5.0

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