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The energy terms in InterfaceAnalyzer

Submitted by Sunyp_IM on Tue, 2021-11-02 18:43
Category: 
Scoring

Dear All,

There are many energy terms in the output of the InterfaceAnalyzer, but is there any articles or other forms of materials  which explain the basic principals or mathematical formats for calculating these energy terms in detail? And How rosetta codes for them? If I wished to add some energy terms in InterfaceAnalyzer, What is an effective way to learn the coding for this propose? 

I will appreciate any help. With many thanks.

 

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Rosetta 3 - Applications

trRosetta - Nan occuring in Hbond calculation

Submitted by y_atsmonraz on Mon, 2021-10-04 09:16
Category: 
Scoring

Hi everyone, 

 I apologize in advance if I am missing out on any critical detail that is relevant for troubleshooting this, but i'm completely new to trRosetta so please bear with me.

Currently, I am trying to run it with an MSA in order to construct an ab initio model for a target protein but I keep running into the following error

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core.scoring.hbonds.hbonds_geom: [ ERROR ] NAN occurred in H-bonding calculations!

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Rosetta 3 - Applications

Help deciphering an input

Submitted by Elijah_Hix on Wed, 2021-09-22 11:12
Category: 
Scoring

Hey all! I am quite new to Rosetta and am using it for a project I am working on. My PI and I have found a paper in which we are wanting to use its code for minimizaiton and repacking but I really do not understand everything that is going on here. The code is as follows:

 

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Rosetta 3 - General

Less silly way to get number of iterations of Relax

Submitted by matteoferla on Tue, 2021-07-20 07:00
Category: 
Scoring

Currently to get the number of iterations a mover, such as FastRelax does, I enable the dump_trajectory scoretype and count the models in the PDBs (code below).

This seems very very weird way of doing this, so I was wondering if there is a less silly way of doing this?

Also, is there a direct way to open a multimodel file say to get the scores of each? (Rather than extracting the models, writing to file, reading them into PyRosetta and scoring them).

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PyRosetta - General

Scoring in Rosetta

Submitted by Elijah_Hix on Wed, 2021-07-14 06:48
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!

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Rosetta 3 - General

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

Submitted by matteoferla on Fri, 2021-07-09 08:36
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

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Rosetta 3 - General

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

Submitted by ericlang on Mon, 2021-07-05 05:43
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.

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Rosetta 3 - General

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