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

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?

Post Situation: 

AddHelixSequenceConstraints Mover2

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

Post Situation: 

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

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 

Post Situation: 

Error compilation Phenix-Rosetta interface

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:

Post Situation: 

protein interface design

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

Post Situation: 

SnugDocking result interpretation

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:

Post Situation: 

Relax with multiple small molecules

Category: 
Small Molecules

Fast relax works fine with two ligands when the .params file are provided in the format.

-extra_res_fa LG1.params LG2.params

But when the same protocol is used with a few added flags such as

-relax:respect_resfile
-packing:resfile resfile

it fails with the following message

Post Situation: 

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