You are here

Unsolved

The problem hasn't been solved

Scoring in Rosetta

Category: 
Scoring

Hey all! I am quite new to Rosetta so I am hoping someone may be able to help. I understand how scoring works in Rosetta and how it is calculated but what I do not know is what a 'good' score is. I am trying to minimize a decently large protein and I don't know what sort of score I should be looking for. Thanks!

Post Situation: 

rosetta_cm segfault

Category: 
Structure prediction

I set up a homology model with the setup_RosettaCM.py
It creates a set of threaded models, an xml file with commands, and a flags command that points to the input file and the xml. When I run the rosetta_scripts command with this flags and xml, I get a segmentation fault. I find the error messages difficult to understand. 

Here is the command, screen output, flags, xml, and CRASH.log

Post Situation: 

Why does the sum of the per-residue total energy not match the whole score?

Category: 
Scoring

At the bottom of a scored PDB file is a POSE_ENERGIES_TABLE. The sum of total, which is already a dot product with the weights, does not match the total score.

Here is an example in Python3, either with or without PyRosetta —This is a question about the C++ not the Python bindinds, hence my posting in Rosetta General

Post Situation: 

How to make .frags files

Category: 
Design

Hello! 

I am working through the online pyrosetta tutorial in jupyter notebooks, and they request you use files that are ".frags" files for ab initio structure prediction. Unfurtunately, all of the google drive files that come with the tutorial are no longer accessible (the link goes to a 404 error).

How do you create these .frags files for your POI? I tried using old robetta, but none of the "fragment" files produced have the .frags extension, nor can any of them be downloaded off of the internet. I would appreciate any help/advice!

Post Situation: 

Differences between energy values reported in the tutorials and the ones obtained by running the code, what is normal?

Category: 
Scoring

Hello, I am new to using Rosetta so appologies for the very basic question

I work with Rosetta version 3.12 and I am following the tutorials: https://www.rosettacommons.org/demos/latest/Home

When I run the examples from the tutorials, the energy values I obtain are significantly different from the results of the tutorial.

Post Situation: 

D-amino acids tripeptide docking.

Category: 
Docking

Dear Rosetta Users, 

I'm going to run a molecular docking simulation of a tripeptide - small protein (around 150 aminoacids) complex.
The tripeptide consists of all D-amino acids and has about 20 rotatable bonds. 

Which application -- between RosettaLigand and FlexPepDock -- is better to dock such a small and high-flexible peptide ?
Moreover, I'd like to know which is the most up-to-date protocol to incorporate non-canonical amino acids into Rosetta.

Thanks in advance!
Samuele  

Post Situation: 

Error running D100_Docking.py

Category: 
Docking

Hello,

So I am trying to run the D100_Docking.py on PyRosetta4 that I have installed on Windows 10 Bash shell. I am just trying to use the script as is before attempting my own PDB files. Below is what I did, along with the errors:

 

Any help is greatly appreciated!

 

(base) jrodriguez@DESKTOP:/mnt/c/Windows/system32$ cd /mnt/c/Users/jrodriguez/Documents/PyRosetta4

Post Situation: 

Pages

Subscribe to RSS - Unsolved