# Design

## Specifying resfile in rosetta scripts

Category:
Design

Hi, I want to design a protein interface by rosetta scripts with the positions I want to mutate stated in a resfile.
However, the output generated included mutations in other positions which were not stated in the resfile.
I wonder if there is something wrong with my scripts.
Would you mind glancing through the following (.xml, flags, resfile and the command of running)?
Thank you very much for your help!!!

1) design_script.xml

Post Situation:

## Two questions on the RosettaScripts flexbb-interfacedesign.xml

Category:
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.

Post Situation:

## Any backrub expert?

Category:
Design

Dear all,

I have just started out my work in a computational protein design lab.
The first algorithm I learned at the beginning was backrub, which I know basically could be used for flexible backbone design.
After using it for a while, I have some doubt in my mind.
Would you mind sharing your valuable experience on the following situations regarding backrub?

1) I have generated 50k structures by backrub.
After removing redundant sequences, the number of unique amino acid sequence was just 1k.

Post Situation:

## Clarify ProteinInterfaceDesign “randomness”

Category:
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

</SCOREFXNS>

<FILTERS>

Post Situation:

## ProteinInterfaceDesign algorithm questions

Category:
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

</SCOREFXNS>

<FILTERS>

Post Situation:

## Error when using "generate_resfile_from_pose" function

Category:
Design

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:

Post Situation:

## Errors in Interface_design_demo

Category:
Design

Hello there,

When I try to run the minpac_optE-premin under interface_design_demo, I got the following error message:

File: src/utility/options/OptionCollection.cc:239
ERROR:

File: src/utility/options/OptionCollection.cc:1324

[ WARNING ] Tried to calculate the visibility of Tracer 'Error' before init() was called!
[ WARNING ] This tracer will not obey commandline options.

Post Situation:

## Error when using RabD with a nanobody.

Category:
Design

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

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

Post Situation:

## Rosetta script to relax a neighborhood only

Category:
Design

I often have a disruptive mutation, say a selection winner has leucine to a proline, where design, backrub and even Remodel (with finding neighbours) give a pose with an empirically discordant poor score. Doing a Relax fixes things, but relax is dangerous as it is may find a better minimum for an unrelated loop (say as a helix).

Post Situation: