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ProteinInterfaceDesign algorithm questions

Category: 
Design

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro.  Thanks in advance

        </SCOREFXNS>

        <FILTERS>

Post Situation: 

make_fragments.pl

Category: 
Fragment Generation

Hi everyone,

           I wanted to let you know about a bug that I was able to fix. if you use the make_fragments.pl in the /rosetta/tools/fragments/ folder it calls another script install_dependencies.pl it calls an online script update_blastdb.pl which in the install_dependencies.pl is at this url:

 

https://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl

 

it returns a 404 error. 

 

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why two packing setting return different energy?

Category: 
PyRosetta

Hello everyone, 

recently, i doing the Exercises of workshop6, but i found i was confused about the packing and design in rosetta...

Anybody can help to figure out why the two setting method of PACK (def pack1 and def pack2) return different energy?it should be the same as i think!

if i run pack1 followed by pack2, then it return the same(lower) energy. it seens that the design energy is not optimized. so should i set another packing after the design? 

thanks if anyone can help.

 

MY CODE: 

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Error with etable_atom_pair_energies()

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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Error when using "generate_resfile_from_pose" function

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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about deNovoProteinMimeticsGen2

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 

Post Situation: 

molfile to params polymer python errors

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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Relax output mmCIF file to a particular path

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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InterfaceAnalyzer packstat score = 0.000

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-based projects using and licensing

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:

Post Situation: 

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