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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

Hydrogen Bonding Distances and Atom identification

Submitted by kmolloy717 on Fri, 2021-06-25 08:15
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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PyRosetta - General

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

Submitted by sgaray on Thu, 2021-06-24 14:47
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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Rosetta 3 - General

Meaning of Metalbinding_constraint

Submitted by Corvin on Wed, 2021-05-19 07:54
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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Rosetta 3 - General

hpatch commands and how to identify patches

Submitted by Bianca Oliva on Thu, 2021-04-29 04:02
Category: 
Scoring

Hi everyone!

I would like to determine the hpatch score for proteins to predict the affinity to lignin as described by "Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity" by Sammond et al 2014 and developed hpatch by Jacak et al.

I tried to validate the method by BSA hpatch but it is not worked (the output was 8.0 whilw should be 36).

I also don't know how to obtain the hydrophobic patch area and how to identify it in protein structure.

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Rosetta 3 - Applications

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