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Category: 
ROSIE

Dear ROSIE2 team,

thank you very much to making available such a great ressource.

I used the ROSIE2 server and AlphaRed to predict protein-protein interactions. While it works most of the time, I would like to share some of the error messages which I experience regularly. Maybe they help you to improve the software.

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AlphaRed job №16676

Post Situation: 

Are catalytic residues mutatable?

Category: 
Enzyme Design
Hi all,

I was running the integration test of the enzyme design (main/tests/integration/tests/enzdes). According to the fifth constraint block in the cstfile at position Trp100 residues WFY with atom type aroC are allowed. However within 150 output structures I never observe a mutation away from the native Trp. In contrast, residue Ser98 is variable in the results (only has backbone constraints). Similarly, I never observe any mutation away from a native catalytic sidechain in my own project.

Post Situation: 

peptide design

Category: 
Design

Hi, 

I have a protien peptide complex and I want to design a peptide that will bind to the protein better the the WT peptide. What tools do you suggest I use? it can also be from

any of the other rosseta platform (or any other). My goal is to find 50 potential peptides and then test them experimentally.

Thanks, 

Miriam

Post Situation: 

rosetta_cm - ERROR: Assertion `tlen < slen` failed on File: src/core/fragment/util.cc:177

Category: 
Structure prediction

I'm following this tutorial to run a protein structure prediction: https://new.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial

I was able to model one protein sequence successfully following those steps, but trying for different ones I've been getting this same error:

Post Situation: 

fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz

Category: 
Structure prediction

Hi,

When I run fragment_picker, it gives the message:

ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
ERROR:: Exit from: src/protocols/frag_picker/VallProvider.cc line: 17
 

the detail message as follows:

Post Situation: 

Post-traslational modifications

Category: 
Chemically Modified Residues

Hello, everyone

I was trying to study the effect of post-translational modifications on the structure of proteins. For that purpose, I followed two different approaches:

  1. I modified the residue with a variant using pyrosetta.rosetta.core.pose.add_variant_type_to_residue. Then, I replaced the original residue with the modified one using pose.replace_residue().

Post Situation: 

Converting all residues to poly-Gly/Ala

Category: 
Enzyme Design

Hey, I am pulling my hair out over this. I am trying to convert all residues in a protein to poly-Gly/Ala (for example 1ae1.pdb) but cannot find the Rosetta function to do so. I am replicating a paper where they included code and output, the output appears to be typical Rosetta output (the .pdbs are like 3tzc___1.pdb) which I am assuming were generated with a Rosetta function.

Post Situation: 

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