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Scoring

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 *

Post Situation: 

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.

Post Situation: 

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!

Post Situation: 

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 ...

Post Situation: 

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.

Post Situation: 

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)?

Post Situation: 

scorefunction Talaris2013

Category: 
Scoring

Hi,

I'd like to use new scorefunction from article by O'Meara et al., 2015, from JCTC. Acording to supplementary info the published ElecHBv2 is the Talaris2013. There is missing line 'yhh_planarity 0.5' in my installation (in comparison with published article). Should I add this line or is it set there by default? what does this line mean.

thanks,
David

Post Situation: 

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