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Show I be using beta_nov16 scorefxn?

Submitted by matteoferla on Thu, 2021-04-01 04:06
Category: 
Scoring

ref2015 is the default at least in pyrosetta and is beta_july15 without the need for the boolean option `correction:beta_july15` to be set.

In the cartesian ddG paper, Park et al. 2016, beta_nov16 is made, which has several difference (below, code used here).

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Rosetta 3 - General

Atom-wise energy terms from nearest N-neighbors

Submitted by jasiozaucha on Thu, 2021-03-25 14:49
Category: 
Scoring

Hello PyRosetta users,

Can you please advise me on how I should go about calculating atom-wise energy terms?

Should I simply sum pairwise energies for the nearest N-neighbours or is there a better way of doing this?

 

Thanks!

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PyRosetta - General

Individual Residue Energy

Submitted by Peik on Fri, 2021-02-19 10:13
Category: 
Scoring

Hi everyone,

I'm trying to get the energies of individual residues in a pose and am encountering an error that I can't seem to find much information on. Here is a sample of my script: 

from pyrosetta import *
from pyrosetta.rosetta import *
from pyrosetta.rosetta.core.scoring import *

pyrosetta.init('-ignore_zero_occupancy false')

pose = pose_from_pdb(pdb_file)

sfxn = create_score_function('ref2015.wts')

score = pose.energies().residue_total_energy(1)

And here is the error I encounter:

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PyRosetta - General

hbond_sr_bb and hbond_lr_bb for different chains

Submitted by tylerborrman on Tue, 2020-10-13 13:41
Category: 
Scoring

In the rosetta scoring function, what energy term describes backbone-backbone hydrogen bonding between residues on different protein chains 

hbond_sr_bb                                Backbone-backbone hbonds close in primary sequence.  All hydrogen bonding terms support canonical and noncanonical types.
hbond_lr_bb                                Backbone-backbone hbonds distant in primary sequence.

 

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Rosetta 3 - Applications

Score function: unable to open input_files/1qys.pdb

Submitted by Cyrrusm on Tue, 2020-10-13 11:35
Category: 
Scoring

Hello all, 

I am new to rosetta trying to follow the tutorials on line. I am currently working on with the mac binaries on MacOS mojave

Seems I cannot generate a score file in the working directory.

the following input is being done within source directory

INPUT: $ROSETTA3/bin/score_jd2.default.macosclangrelease -in:file:s input_files/1qys.pdb

 

Error:

ERROR: Cannot open file "input_files/1qys.pdb"

ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 362

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Rosetta 3 - General

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