Design

I am trying to use flexbb-interfacedesign.xml from rosetta 3.9 to do the design of a protein interface.

I have two questions:

1) The top of flexbb-interfacedesign.xml reads as the following, is there a missing open bracket before "ProteinInterfaceDesign...", as highlighted in red?
2) How does rosetta define "chain1" and "chain2", as highlighted in yellow? I have tried many times by changing either "1" or "0" and even changing the chain name in the pdb (e.g. A->B, B->A) but still I cannot control which chain to design.

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro. Thanks in advance

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hello every one,

I am learning how to use pyrosetta, when i study the workshop6, i meet a problem about generate_resfile_from_pose function.

My code:

from pyrosetta import *

from pyrosetta.toolbox import generate_resfile_from_pdb, generate_resfile_from_pose, mutate_residue

pose = pose_from_pdb('ref.pdb')
pymover.apply(pose)

# scoring
score = create_score_function("ref2015")

generate_resfile_from_pose(pose, 'pose.resfile')

the error returns to me:

Hi Everyone,

Recently, I am using RabD to design my nanobodies, But I can not perform it smoothly:

>>>Error returns:

ERROR] Exception caught by JobDistributor for job complex.1_0001

File: src/protocols/antibody/AntibodyInfo.cc:1117

L1 start resnum not found in pose: 24 L

Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB.