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Fusing C-terminal or N-terminal segments onto proteins using Remodel

Category: 
Structure prediction
Design
Loop Modeling

Hi I am trying to fuse a structure onto a designed protein structure at the C-terminus using the following command:

remodel.linuxgccrelease -s model3.pdb -remodel:RemodelLoopMover:bypass_closure -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -num_trajectory 3 -save_top 1 -database <PATH> -overwrite -out:file:scorefile model3.sc

model3.pdb covers the range: 1-393

model4 covers the range: 290 - 393

Where the blueprint has the following general format:

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Fusing C-terminal or N-terminal segments onto proteins using Remodel

Category: 
Design
Loop Modeling

Hi, I am trying to replace the C-terminal segment of a designed protein with that taken from a crystral structure using the Remodel module with the DomainFusion flag turned on. I have tried several different tweaks to the arrangment however the gist of it is that I use the following command. 

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Fixing part of a ligand in dock-design

Category: 
Docking
Design

Hi,

 

I am using a dock-design protocol to design a binding pocket to bind a ligand. I know where parts of the ligand should bind (orinetations and the position in protein) but the other parts can be flexible. Right now after the dock and design protocol, most of my outcomes change the whole position of ligand and don't keep that part fixed. Is there a way to tell the program to keep parts of the ligand fixed? or a way to generate conformers for only parts of the ligand? 

 

Thanks.

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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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