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Side-chain grafting at the fixed protein and position

Category: 
Design

Hello folks,

I’m trying to transfer a epitope to the protein of my interest at the designated position which is composed of alphahelix. 

Previously, several antibodies have been shown to recognize the alphahelical conformation such as PDB:3LRH. 

So I wonder if I can transfer the epitope to the designated position while keeping its ability that is recognized by the corresponding antibody. That is something like

Post Situation: 

Side-chain grafting in fixed scaffold

Category: 
Design

Hello folks,

I’m trying to transfer a epitope to the protein of my interest at the designated position which is composed of alphahelix. 

Previously, several antibodies have been shown to recognize the alphahelical conformation such as PDB:3LRH. 

So I wonder if I can transfer the epitope to the designated position while keeping its ability that is recognized by the corresponding antibody. That is something like

Post Situation: 

Multistate design issues with -run:msd_job_dist option and MSDMover

Category: 
Design

Hi there,

I'm trying to perform multistate design using Rosetta 3.11 to improve antibody binding to five slightly different epitopes. I've been following the tutorial provided by the Meiler Lab and I've been able to successfully prepare my input files, but I'm having issues running the design.

First, when I tried to run the design using the attached .options and .xml files, but I got the following error:

Post Situation: 

Error with filter in rosseta_scripts

Category: 
Design

Hi 

i am working inthe design of peptides using the genkic mover. I am trying to implement a filter with "PeptideInternalHbondsFilter" to remove unwanted structures. When i run the rosetta_scripts  command this is the output.

From line 42:
Error: Element 'PeptideInternalHbondsFilter': This element is not expected.

Post Situation: 

BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?

Category: 
Design

I triple checked my protein PDB file, and i used the script to get a blueprint file. It has no chain definitions and is perfectly in order. Error happens when a succesful closure is made. If the closure is not successful, it continues. Also, if i set G or POLAR instead of ALLA, it works.

Post Situation: 

RosettaDesign error with Option file open failed

Category: 
Design

Dear users and developers,

I was running RosettaDesign and an error was reported as "[FILE]: src/utility/options/OptionCollection.cc

[LINE]: 536

[START_MESSAGE]

Option file open failed for: '/**/general_FD.flags'".  

This flag file worked on other server previously. Is this an error with compiling Rosetta or with the flag file? Could anyone please give some suggestions about how to fix this? Thank you so much.

Best,

Post Situation: 

Breaking fastDesign into more stages or writing something custom

Category: 
Design

I know that rosetta_scripts XML protocols can be run in PyRosetta, and I think there is also a specfic PyRosetta version of fastDesign.  But I'm wondering to what extent the underlying functions used in fastDesign (e.g. modifying constraint strengths, modifying vdw repulsion terms) can be written in PyRosetta directly such that some customization would be possible?

 

Post Situation: 

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