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Filter for fixed-bb design using RosettaScript?

Submitted by chrisHKL on Fri, 2020-02-28 19:47
Category: 
Design

Hello,

If I want to implement fix-bb design (or a slight variation of it) using RosettaScripts, what filter should I use?

Can I not use a filter if I'm just interested in generating a library of designs from multiple input structures with different backbone conformations?

Does it make sense to not use a filter, since (to my understanding) the packer will generally pick rotamers that have less energy than the original residue anyways and output a final score for the designed pose?

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Rosetta 3 - Applications

Ddg filter threshold value?

Submitted by chrisHKL on Fri, 2020-02-28 15:01
Category: 
Design

I am doing protein-protein interface design using RosettaScripts, and in the .xml file under the demo at:

ROSETTAPATH/demos/public/rosetta_scripts_pp-interfacedesign/scripts

It has the following line: 

<Ddg name="ddG" scorefxn="talaris2014" threshold="-15" repeats="2"/> binding energy calculation; an average of two repeats is computed for better numerical accuracy

 

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Rosetta 3 - Applications

What is interface_cutoff_distance? And why did my residues outside this value get designed?

Submitted by chrisHKL on Fri, 2020-02-28 14:52
Category: 
Design

Under the description for the mover RepackMinimize:(https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/RepackMinimizeMover)

it says "interface_cutoff_distance: Residues farther away from the interface than this cutoff will not be designed or minimized."

However, what is "the interface"? Is it:

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Rosetta 3 - Applications

PyMOLMover not working in conda

Submitted by FenrisDaWolfff on Fri, 2020-02-28 00:18
Category: 
Compilation

Hi,

I just set up everything in conda environment, and everything seems working great, except that I can't get pymol mover working - when I run PyMOLRosettaServer.py, I get:

PyMOL not running, entering library mode (experimental)

pyMOL <---> PyRosetta link started!

at 127.0.0.1 port 65000

despite that my pymol is running perfectly fine. What should I do to make pymol mover work? Any help would be very appreciated.

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PyRosetta - Build/Install

Are 100 structures the maximum generated when using homology_with_end_extension (broker protocol)?

Submitted by thaisarns on Fri, 2020-02-21 05:46
Category: 
Structure prediction

Hi!

I have one protein that I would like to model ab initio the final 29 residues (1 - 160 is fixed/I have the x-ray crystallography model,  161 - 189 is the region to be modeled).

I am using the following parameters:

- protein.tpb

CLAIMER RigidChunkClaimer

REGION_FILE protein.region

PDB_FILE protein.pdb

END_CLAIMER

- protein.region

RIGID 1 160 0 0 0

- the command I ran :

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Rosetta 3 - General

dump_scored_pdb

Submitted by allan.ferrari on Wed, 2020-02-19 07:21
Category: 
Scoring

I am new to Pyrosetta and trying to dump the modified pose along with its total energy.

I have used pose.dump_score_pdb('model.pdb', scorefxn) to have the total score printed out with the PDB file.

However, this method prints out way more information. What would be the equivalent way of having the total score printed out (as the fileters work in the xml file at rosetta scripts)?

 

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PyRosetta - Scripts

Does it make sense to perform Docking on a complex?

Submitted by chrisHKL on Mon, 2020-02-17 09:12
Category: 
Design

I am trying to design an orthogonal ligand/receptor system. I've inherited the script below as a starting point but I'm wondering what exactly the Docking mover would be doing. My PDB structure is a ligand that is already bound to the binding domains on the receptor. Does it still make sense to perform a docking step in this scenario?

My script:

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Rosetta 3 - General

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