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Scoring

RASREC - finding lowest energy structure

Category: 
Scoring

Hi Rosetta community,

After finally getting the RASREC run to successfully generate full 6 stages, now I'm at the point where I want to score the pdbs to find the lowest energy structures which suppose to be the closest to the native structure. But in this website: https://www.rosettacommons.org/demos/latest/protocol_capture/rasrec_evolutionary_restraints/README

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How does Rosetta select atom pairs for Lennard Jones Potential calculations?

Category: 
Scoring

Hi,

I am a new user for Rosetta and I am now trying to figure out how exactly PyRosetta is making the atom pair selection for scoring function calculations in general. For example, when we calculate pair-potential we will not include those bonded atom pairs and we also do not consider those who are two chemical bonds away. I wonder what is the selection rule for Rosetta? And where I could find the source code in the Rosetta folder?

 

Many thanks.

 

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How to determine interface residues

Category: 
Scoring
PyRosetta

Hi,

I have a couple questions about fold-trees and how interfaces are calculated in pyrosetta (or rosetta).  I have a structure of an antibody-antigen that I have prepared using rosetta (attached).  A visual inspection shows that residue B:TYR210 is making a number of close contacts with residues in Chain C (the antigen).  However, when I construct an Interface object in pyrosetta, this residue is not identified as being in the interface (using a cutoff of 5.0A):

 

from rosetta import *

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pose.replace_residue() & incorrect scoring

Category: 
Design
Scoring

Hi developers,

I wasn't sure where to submit bug reports so I'm posting here instead.

I've noticed a scoring error after repeated pose.replace_residue() function calls. The final pose after repeated calls to replace_residue() ends up having a score substantially lower (often < -50 Rosetta energy units) than when scored using the scoring application or if the pose is loaded upon application initialization.

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Rosetta Holes

Category: 
Scoring

Dear Rosetta Users:

I would like to use the rosetta holes application to evaluate the packing of my protein. But the documentation for this aplication is not in great details. I have been searching posted questions about rosetta holes from the forum and it seems that this app has been in and out of the rosetta suite. So I am wondering if the rosetta holes is currently available in the most updated rosetta version and if there is a general guide on how to use this application.

Thank you very much!

Best regards,

zsun12

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Per residue scoring

Category: 
Scoring

Hi all,

I want to be able to get score information for individual residues from my decoys. What is the easiest way to do this currently? I couldn't find a relevant option in the documentation, do I have to use RosettaScripts or something? I found some old posts on this topic, but I figured I'd ask again in case things have changed in more recent versions.

Thanks!

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Error Scoring Application- Illegal attempt to score

Category: 
Scoring

Dear users
I'd tried to analyse my silent file that came from other concatenated silent files (cat *.out > 5novo.out) running the scoring application through my command line [1] but the program gave me this message:
...
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 420 in file 1IYT.pdb. Best match rsd_type: ALA_p:CtermProteinFull
core.pack.task: Packer task: initialize from command line()
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...

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Interpreting decoy ensemble

Category: 
Scoring

When interpreting an ensemble of decoys made with relax or backrub, which structures should be discarded and which ones retained. I get a lot of conflicting advice ranging from “keep them all” to “take the top 10%”. Is there a best practice regarding this?
Also, should the structures be clustered and only the centroids considered?
Any advice would be of help.

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Should I trust the score output from relax used with a protein complex?

Category: 
Scoring

I am using the relax.linuxgccrelease application to relax a protein complex. I simply send the pdb containing all of the fomed complex to relax.

The score outputted by relax represents the sum of the score of folding plus complex formation (in Rosetta arbitrary units, of course)?

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