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Problems with output control

Submitted by Sunyp_IM on Thu, 2017-06-22 15:30
Category: 
Compilation

Dear all,

I am new to rosetta. I am studying the Rosetta tutorials and I am there is a problem with output path control. I followed the tutorial 4 (controlling input and output) and type the following command in the section "Setting output paths" of this tutorial into my CentOS 7 linux shell:

$> $ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb -out:pdb -out:path output_files

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Rosetta 3 - General

generate_nonstandard_residue_set Exception

Submitted by lah435 on Tue, 2017-06-13 18:28
Category: 
PyRosetta

generate_nonstandard_residue_set is giving me an error I don't understand. Can anyone tell what I'm doing wrong here?

In [2]: %paste
from rosetta import *
from pyrosetta import *
init()
params_paths = utility.vector1_string()
params_paths.extend(["GUA.params"])

In [3]: nonstandard_residue_set = generate_nonstandard_residue_set( params_paths )
---------------------------------------------------------------------------

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PyRosetta - General

Total score for individual residue

Submitted by ac.research on Tue, 2017-06-06 05:24
Category: 
Scoring

Dear PyRosetta People,

 

I am trying to find the total score of an individual residue. This is my script so far:

 

scorefxn = get_fa_scorefxn()
scorefxn(pose)
AA_Score = pose.energies().residue_total_energies(5)
print(AA_Score)

 

It seems i get a massive print out, and when repeated for different residues gives the exact same values, so i am sure my script is wrong.

 

What is the correct way to get the total score for just 1 amino acid?

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PyRosetta - Scripts

Cutout part of a protein

Submitted by ac.research on Wed, 2017-05-31 11:55
Category: 
PyRosetta

Hello People,

 

I am trying to find a way to cut out part of a protein and save to a new .pdb file.

 

So i have a protein and i want to cut out a section (from amino acid 315 to 330 for example), and save that cut out (and maintain the original 3D structure) into a new .pdb file.

 

I tried searching if there is a built-in PyRosetta function/method that does this, or if there is a script that does this, but i could not find.

 

Anyone can help me or guide me?

 

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PyRosetta - General

Creating rotamers, computing pairwise and total energies

Submitted by gerdos on Wed, 2017-04-12 02:57
Category: 
PyRosetta

I just started working with PyRosetta, and i stumbled upon a lot of questions.

I would like to introduce rotamers, and calculate their pairwise energies, and the total energy of the system with given rotamers.

To test, i created a very simple PDB that consist only 2 amino acid. 

I have the following code:

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PyRosetta - General

Docking Prepack protocol working or not ?

Submitted by MJG on Mon, 2017-04-03 08:02
Category: 
Docking
Scoring

Hi Rosetta community, 

I'm running the prepack protocol using as input a PDB file containing a dimer (chain A and B). The protocol seemed to work ("... reported success in 3 seconds") but I get the following warning : 

[ WARNING ] When switching to a fa_standard ResidueTypeSet:  Pose already contains fa_standard ResidueTypes.

and my score_sc file contains 0.000 for the total score for every generated structure.

Here the command I used to run prepack:

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Rosetta 3 - Applications

constraints

Submitted by lah435 on Sun, 2017-03-12 03:25
Category: 
Nucleic Acids

My pose has DNA strands and I am trying to constrain the blunt ends.

Each DNA chain is numbered starting from 1. Why can't Rosetta find the atoms?

Here is my constraint:

AtomPair C1* 1C  C1* 35D  HARMONIC 12.028 1.00

And here is the error:

[ERROR] Exception caught by JobDistributor for job VGK8_v2_0001Atom 'C1* 1359' not found

 

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Rosetta 3 - General

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