# Design

## 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

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## 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:

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## 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.

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## 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.

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## 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).

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## ProteinInterfaceMS

Category:
Design

Hello,

I have been running the ProteinInterfaceMS mover with rosettascripts. It runs successfully, though one single design seems to take about 5 days to complete. This is on one cpu. I was wondering if ProteinInterfaceMS mover is capable of making use of MPI? If so how does it split the calculations? And how would you submit the command?

Thanks

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## Error in enzyme_design.default.linuxgccrelease: corrupted size vs. prev_size

Category:
Design
Enzyme Design

Dear Rosetta Team,

I am trying to run enzyme design protocol on protein model with 2 Iron ions, 2 Ions, 1 molecule and 1 water molecule (!). Problem is it is getting core dump/segmentation fault each time I run it. After various code recompilations and printing the error I came came to know the error is at "EnzdesBaseProtocol::enzdes_pack(" in EnzdesBaseProtocol.cc.

code:

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## cartesian_ddg output

Category:
Design

I am following the protocol

to predict the ddG of a monomer after a point mutation. I am using Rosetta 3.10.

The output file, mutfile.ddg, looks like this:

COMPLEX:  Round1: WT ...

COMPLEX:  Round2: WT ...

COMPLEX:  Round1: MUT_1ALA ...

etc.

Instead of COMPLEX, I was expecting to see lines beginning with

BEFORE_JUMP: RoundX:

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