You are here

Design

get an increased energy after energy minimization when using different score functions for repacking and energy minimization

Category: 
Design

Hi, 

I am a new user of rosetta. Now I meet some problem that I cannot solve. I am wondering whether you could please help me. I would much appreciated. 

Post Situation: 

MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"

Category: 
Design

Hello everyone,

I am trying to use MotifGraft mover to graft an epitope to a scaffold protein (actually there is a structure library, parsed with -l list).

The xml script is attached.

My command line is as follow (I am first trying a very loose boundary conditions, I'm aware about the higher RMSD/atom_clash values):

Post Situation: 

ROSETTA design affinity optimization

Category: 
Design

Hello

I'm trying to to use rosetta design (http://rosettadesign.med.unc.edu) to increase binding affinity between 2 proteins in 1 pdb file. 

I want 2 residue ranges to be mutated in chain B but all other residues to remain the same. Therefore I have used this resfile:

NATRO

start
71 - 88 B ALLAAxc EX1
50 - 56 B ALLAAxc EX1
 

However, the server mutates residues in both chains. How do I force it to only mutate chain B?

Post Situation: 

fixing sequence during grafting in antibody_designer

Category: 
Design

Using antibody_designer to graft loops on one CDR. I'd like to fix the sequence of the grafted loop to native. It appears to ignore the 

I have tried something like this in my cdr_instruction file

H3 GraftDesign ALLOW

ALL SeqDesign FIX

 I've also tried passing it a resfile forcing everything to be native like so

NATAA

start

Post Situation: 

Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

Post Situation: 

Rosetta Resfile header

Category: 
Design

I have been using Rosetta design for quite a while but I did not pay attention to what Resfile header would do. I looked for descriptions and examples files different people have shared and used and I am unable to understand when I should specify NATRO or NATAA in the header?

I want to perform different tasks. For example:

1) Mutate specific residue to ALLAA and I use header like:

NATRO
start
30 H ALLAA

whereas, I found someone using following header:

Post Situation: 

Error during single state design

Category: 
Design

Hi,

During single state design of protein the following error is encountered after relaxing the structure at the fixed backbone design stage  and also by design iterated by backrub motion.

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job 4MUI_relax_design_0010

Post Situation: 

Seasons greetings with a Christmas tree shaped protein

Category: 
Design

For outreach, I made a spinning and blinking FITC-labelled Christmas tree (https://michelanglo.sgc.ox.ac.uk/r/christmas) using various Rosetta tools, which I have learnt to use properly thanks to all of you.

So using the excuse of the cheer of the holiday season, I wanted to sincerely thank all of you for all the help I have recieved in this forum! It has been invaluable and I really mean it.

Post Situation: 

Pages

Subscribe to RSS - Design