# Scoring

## ref2015: approx. kcal/mol or actually kJ/mol?

Category:
Scoring

This may be a really dumb question, but I am struggling to make sense of some data —so any input is welcome.

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## trRosetta - Nan occuring in Hbond calculation

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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## Help deciphering an input

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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## Explicit water

Category:
Scoring

Hello,

I have a pdb with crystallographic waters which appear to be important for the protein structure, and perhaps function. I am generating mutations using pyrosetta and evaluting their relative scores, and exporting structures to be simulated with MD.

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## Less silly way to get number of iterations of Relax

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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## 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!

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## 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

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## 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.

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## Hydrogen Bonding Distances and Atom identification

Category:
Scoring

We are using PyRosetta 2.83 to identify hydrogen bonds between atoms.  For example, take the following code:

pose = pose_from_pdb("/Users/kmolloy/Downloads/2ezk.pdb")
hbond_set = pose.get_hbonds()
hbond_set.show(pose, 5)
hbond_set.show(pose,7)

This results of running this code are shown below:

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