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Scoring

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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Error using ddg_monomer application (Assertion `pose.residue(resnum).name1() == wt` failed)

Category: 
Scoring

Hi, I've unsuccessfully tried to run ddg_monomer app. I want to study the estability of a small protein after some mutations. I have used a pre-minimized pdb file as an input file, but I have the following error (last lines):

apps.public.ddg.ddg_monomer: reading in mutfile
apps.public.ddg.ddg_monomer: wt is N resnum is 25 and mut is P
apps.public.ddg.ddg_monomer: wt is Y resnum is 60 and mut is H

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Meaning of Metalbinding_constraint

Category: 
Docking
Scoring

Dear Sir and Madam,

Would anyone here be kind to explain the following statement about metalbinding_constraint or send the relevant paper?:

1. The (bio)physical meaning of metalbinding_constraint. I would like to find out, the underlied forces and energies, including such thermodynamical parametres, as enthropy, enthalpy and so on and so forth. Hereby, the next question arises from this point.

2. How this 'metalbinding_constraint' is calculated (I mean the formula, but, nevertheless, I am open to any explanation).

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