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How to run PLOT LHOC on Results from Rosie Server

Submitted by sujigeorge1979 on Mon, 2019-06-10 19:32
Category: 
ROSIE

Hi,

 I am using Rosie antibody server for modeling antibody. In order to validate the model i need to run the PLOT LHOC script on the output results from Rosie server. However while running the script i am only getting the graph for the final model and not the template. kindly can anybody share the comand for running the PLOT LHOC script. Also whether the template used for the calculation by PLOT LHOC is grafted model or the original template PDB.

Thanking you

Dr. Suji george  

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Unsolved
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ROSIE - General

Membrane ab-initio modelling of a beta-strand

Submitted by hzhekova on Mon, 2019-06-10 14:22
Category: 
Structure prediction

Hello everyone!

We're trying to model a membrane peptide of ~50 aminoacids which likely assumes beta-strand conformation in the membrane. Can we do this with the current Ab Initio membrane implementation of Rosetta? I know that we should use Octopus to generate a span file, but I'm left with the impression that it's designed for alpha helical proteins and that Rosetta in general is biased toward generation of alpha helices. Is there a way to enforce some beta-sheet restrictions during the ab initio folding process?

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Rosetta 3 - Applications

How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior )

Submitted by asbelx on Sat, 2019-06-08 00:07
Category: 
Docking

Hello, I want to design my protein wit XML script as the paper  Rosetta and the Design of Ligand Binding Sites
 

I want to dock with ligand.wts(-restore_pre_talaris_2013_behavior ) 

and design protein with ref2015.wts.

But the option -restore_pre_talaris_2013_behavior seem to have impact in ref2015.wts.

How can I solve it?

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Rosetta 3 - Applications

AddHelixSequenceConstraints Mover2

Submitted by Negarsardar on Sat, 2019-06-01 01:54
Category: 
Design

Hello All

I want to design the interface of a two-chain complex( actually design only one of the partner)  using raf / rac design script which I have attached it here.

Is it better and more accurate to change this script in order to get and use resfile ? 

I prefer to design interface automatically without resfile (just script defines interface residues)  because I have no idea about which residues in interface should be designed or not. or what types of mutations are allowable

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Rosetta 3 - Applications

File specification of binary part of silent file (especially PDB section)

Submitted by m.ebert on Wed, 2019-05-29 01:52
Category: 
Design

Hi there,

I would like to know if somebody could share the binary file format specification of the silent file. I try to read the PDB section without any luck. Before digging through the code of extract_pdb I thought it would be faster to quickly ask how to read the binary section.

Thank you very much.

Cheers,

Max 

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Rosetta 3 - General

Error compilation Phenix-Rosetta interface

Submitted by karenjgonzalez on Tue, 2019-05-28 12:40
Category: 
Compilation

Hello!

I have been trying to set up the Phenix-Rosetta interface (phenix.rosetta.run_phenix_interface) by compiling rosetta (rosetta_bin_linux_2019.14.60699_bundle) with the command: ./scons.py -j4 bin mode=release extras=python. However, I get the following error:

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Rosetta 3 - Build/Install

protein interface design

Submitted by Negarsardar on Tue, 2019-05-28 07:04
Category: 
Design

Hello All

I want to design the interface of a two-chain complex( actually design only one of the partner)  using raf / rac design script which I have attached it here.

Is it better and more accurate to change this script in order to get and use resfile ? 

I prefer to design interface automatically without resfile (just script defines interface residues)  because I have no idea about which residues in interface should be designed or not. or what types of mutations are allowable

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Forums: 
Rosetta 3 - Applications

SnugDocking result interpretation

Submitted by jessye on Mon, 2019-05-27 03:43
Category: 
Docking

Hi there:

I use snugDocking to Dock different antibody- antigens.  I wonder how could I determine good binding vs bad binding from the result web page.

I am currently decide by look at 1. interface score 2, similarity of top 10 models.  If the interface score is low and top 10 models have a couples model in similar position, I assume it is good binding, otherwise It isn't

give an example:

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ROSIE - General

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