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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.

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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:

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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

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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.

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Issue with Rosetta LinkResidues Script

Category: 
Design

Hi All,

I am trying to design a 2 fold-symmetrical protein where I want to design a selected number of residues in each half and not mutate the remaining residues in both the halves. For e.g., what I want Rosetta to do is in "Half-A, the residues at position 32, 49, 56, 65, 66 should be mutated to certain residues, and the exact same mutated residues should appear after designing position 32, 49, 56, 65, 66 in Half-B.

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Linear peptide versus cyclic peptide binding prediction

Category: 
Design

I have used ROSIE server to analyze protein-antibody interaction and predict peptide sequences of antibody that would interact with the protein.

The analysis revealed 3 hotspots of the antibody sequence as in the picture attached. It did make sense to me that the predicted linaer peptides from antibody sequence were chosen from 1st and 3rd hotspots from the figure with highest contact points with the protein.

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Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.

Category: 
Design

Dear caretakers/kind strangers,

I ran into an error that i do not understand when trying to do de-novo modelling of a helix linker using REMODEL. When i leave the blueprint file without any new residues it runs fine. But when i add new residues at the end (C Terminal) the program recognizes it is a C terminal extension, but throws this error. 

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Symmetry mode in Remodel for N-terminal extension

Category: 
Design
Loop Modeling
Symmetry

Hello, 

I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error: 

File: src/protocols/loops/loops_main.cc:253
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.

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Errors in Interface design  

Category: 
Design

Hello there, Now I'm trying to optimize the protein sequence at binding interface for increased affinity to its target. A complex structure was previously solved by X-ray crystallography (PDB 3rh8). To make their affinity higher, I would like to design the protein sequence at both sides. Meiler Lab provides a step-by-step tutorial at his website (http://www.meilerlab.org/index.php/rosetta-tutorials). According to his tutorial, I tried, but I found something like error.

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running in MPI mode and multiple scores per output PDB file?

Category: 
Design
Scoring

Hi Forum 
I recently did a Rosetta fixbb run with MPI and found that the score file had a lot more lines of output than there were actual PDB files. Specifically, I've got 353 scores in score.sc but only 12 PDB files.  is it possible that the parallel processors are simply overwriting the PDBs?   Is there a flag I should be including to avoid this? 

Thanks!  

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