The problem hasn't been solved
Hello, I use the rosetta VIP.
I can not understand the option -cp:skip_relax.
If it appear in the flag, will the option -cp:relax_mover and -cp:local_relax be invalid?
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?
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
Hello all
I want to design interface of a complex which contains only alpha helices ( has not any betta strand) , it is important for me that the secondary structures of alpha helices would not be disturbed during sequence 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
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:
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
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:
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
I have successfully installed PyRosetta via anaconda by command of "conda install pyrosetta" in Linux (Windows subsystem Linux) according to this instruction.
