You are here

Home

Scoring

rama vs p_aa_pp vs ref score terms

Submitted by jharamesh on Thu, 2015-12-03 14:24
Category: 
Scoring

Do these three terms in Score12.wts_patch and after have significant overlap?

How would one go ahead to explain a delta_delta_G upon a mutation that has contributon coming from these terms? In one protein case, three mutations T61N, H135Y and H257P, showed significant gain in half-life. The score terms show contribution from Rama, p_aa_pp and ref. 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

RASREC - finding lowest energy structure

Submitted by Lati on Fri, 2015-11-20 03:08
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

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

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

Submitted by bowang2013 on Thu, 2015-10-29 08:04
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.

 

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

How to determine interface residues

Submitted by rbehan on Wed, 2015-10-14 11:25
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: 
Unsolved
Forums: 
PyRosetta - General

pose.replace_residue() & incorrect scoring

Submitted by msun on Tue, 2015-10-06 10:51
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: 
Unsolved
Forums: 
PyRosetta - General

Rosetta Holes

Submitted by zsun12 on Wed, 2015-09-30 11:40
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

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Per residue scoring

Submitted by chelsell on Mon, 2015-08-17 14:43
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: 
Unsolved
Forums: 
Rosetta 3 - Applications

Error Scoring Application- Illegal attempt to score

Submitted by samuelrpita on Thu, 2015-08-06 14:45
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: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Scoring