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Error with etable_atom_pair_energies()

Submitted by yijietseng on Mon, 2019-01-28 14:00
Category: 
Scoring

I am new to Pyrosetta and programing and I am learning how to use Pyrosetta. So when I was practicing scoring with Workshop #3 bullet point 5, I came across a error, and I have no idea what's wrong with.

Here is what I did. 

r1 = pose.residue(24)

r2 = pose.residue(20)

a1 = r1.atom("N")

a2 = r1.atom("O")

etable_atom_pair_energies(a1, a2, scorefxn)

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PyRosetta - General

Error when using "generate_resfile_from_pose" function

Submitted by zhangying1990 on Fri, 2019-01-25 00:45
Category: 
Design

hello every one,

I am learning how to use pyrosetta, when i study the workshop6, i meet a problem about generate_resfile_from_pose function.

 

My code: 

from pyrosetta import *
from pyrosetta.toolbox import generate_resfile_from_pdb, generate_resfile_from_pose, mutate_residue
pose = pose_from_pdb('ref.pdb')
pymover.apply(pose)

# scoring
score = create_score_function("ref2015")

generate_resfile_from_pose(pose, 'pose.resfile')

 

 

the error returns to me:

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PyRosetta - General

about deNovoProteinMimeticsGen2

Submitted by zhangying1990 on Mon, 2019-01-14 17:09
Category: 
PyRosetta

Good morning everyone~ 

Recently, I had read the paper entitled "De novo design of potent and selective mimics of IL-2 and IL-15”

And I am very interesting in it, and I want to learning how to performing it in using pyrosetta. 

However, in the Code availability section, I can not find any information about the submodule 

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PyRosetta - Scripts

molfile to params polymer python errors

Submitted by tsztain on Sun, 2018-12-02 15:38
Category: 
Chemically Modified Residues

I am trying to generate parameters for a non-cannonical amino acid using the molfile_to_params_polymer.py script using python 2.7.5.python molfile_to_params_polymer.py --clobber --polymer --no-pdb --name OCT -k OCT.kin OCT.mol

Edit: this is where I found the python script that is giving the errors.  /path/rosetta_demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py

I get the error:

Traceback (most recent call last):

  File "test_molfile_to_params_polymer.py", line 1995, in <module>

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Rosetta 3 - Applications

Relax output mmCIF file to a particular path

Submitted by AJVincelli on Sun, 2018-11-25 11:04
Category: 
Structure prediction

Hello, how can I specify the path of a Relax output mmCIF file?

I know that I can specify the path of a Relax output pdb file using the flag "-out:path:pdb Sample/Subdirectory." I can specify the Relax output to be an mmCIF file with the flag "-out:mmCIF." However, the flag "-out:path:mmCIF Sample/Subdirectory" doesn't work. When I do this, I get a pdb file in the current working directory, and a message that says "The following options have been set, but have not yet been used: -out:path:mmCIF Sample/Subdirectory/"

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Rosetta 3 - General

InterfaceAnalyzer packstat score = 0.000

Submitted by vmc99 on Fri, 2018-11-16 11:30
Category: 
Scoring

Hello

I am using the InterfaceAnalyzer to obtain packing scores of antibody-antigen strucutres from the PDB database but the packstat score always ends up being 0 for some reason. I am specifying for the activation of packstat calculation as can be seen in my flags.txt file below

-in:file:s 1A14_atomlines.pdb
-interface HL_N
-compute_packstat = 1
-out:file:score_only 1a14_interface.out

The output file is attached below. 

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Rosetta 3 - General

Rosetta-based projects using and licensing

Submitted by SergeyP on Fri, 2018-10-26 15:45
Category: 
Compilation

Dear Rosetta Team,

Is it possible to share a code of my Rosetta-dependent non-profit research project and upload it to a publicly accessible GitHub repository licensed under open source license? Is Rosetta License restricts that?

For example, I have "project" like this:

1. Source files that links to Rosetta headers:

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Rosetta 3 - General

SPLINE EPR_DISTANCE Constraint Error

Submitted by mmw88 on Tue, 2018-09-18 14:39
Category: 
Scoring

Hello,

I'm getting an unusal error when using SPLINE EPR_DISTANCE constraints with the score.linuxgccrelease function. I generated some structures ab initio using SPLINE EPR_DISTANCE constraints with rosetta_scripts.linuxgccrelease and I wanted to rescore the binary output file with some different constraint weights using score.linuxgccrelease. However, if my input constraint file (cst_fa_file) to the score.linuxgccrelease release function contains any SPLINE EPR_DISTANCE constraints, I get:

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Rosetta 3 - Applications

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