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[dev] examples for implementing setup_for_packing, prepare_rotamers_for_packing?

Submitted by ipetrik_ambry on Mon, 2017-10-30 17:03
Category: 
Scoring

Hey,

Can anyone point me to good examples of implmentations for setup_for_packing and prepare_rotamers_for_packing (and I guess update_residue_for_packing while I'm at it)? I'm not entirely sure I understand what the arguments are for these methods and the use case for when I would want to implement these methods.

Thanks in advance!

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Rosetta 3 - General

[dev] determine which score_type's enabled in create_energy_method?

Submitted by ipetrik_ambry on Fri, 2017-10-27 15:37
Category: 
Scoring

Hey,

I have created an energy method and it works. However, I want to do a check at the time it is created for whether a particular score_type is enabled. Is there any way to know which score_types are enabled from within my create_energy_method function?

Thanks!

- Igor

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Rosetta 3 - General

Ineffective Constraints

Submitted by Sandy on Tue, 2017-09-05 19:36
Category: 
Scoring

Hi all,

I am attempting to use Rosetta 3.8 (2017.29.59598) AbinitioRelax with some constraints I have defined, but I get the feeling that the constraints are not being properly implemented. In particular, I attempt to implement a single harmonic constraint using a constraint file with this line:

AtomPair CA 1 CA 41 HARMONIC 55.0 .1

My flags are:

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Rosetta 3 - General

Packstat application output

Submitted by Vedasheersh on Mon, 2017-07-03 02:45
Category: 
Scoring

Hello!

I am trying to use the packstat application for measuring the quality of my model. But, I'm not sure what the terms in output mean? (there is no info in user guide/documentation). I came up with the flags I've used from the RosettaHoles2 paper. As per the paper, it should output some pdb and also output explicit representation of voids. But, I donot see any output files. I only get the commandline output with three score columns.

Could someone clarify?

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Rosetta 3 - Applications

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

Energy scores of D-amino acids

Submitted by jshen2 on Mon, 2017-05-08 10:15
Category: 
Scoring

I used PyMOL and Maestro to invert the chirality of single L-amino acids into D-amino acids, as well as all L-residue polypeptide to all D-residue polypeptides. Even though they are mutually mirror images, but D-amino acids and D-polypeptides all have remarkably higher energy scores than their counterparts by using PyRosetta scoring protocol. May I ask what are some possible reasons for this difference? I am wondering whether it is caused by computational error or more delicate design, such as strong and weak nuclear forces, in Rosetta tool.

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PyRosetta - General

optimisation of a protein-protein interface

Submitted by sdh_h on Thu, 2017-05-04 05:06
Category: 
Design
Scoring
Symmetry

Dear Rosetta users,

I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers. I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.

My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?

Thanks for help! Staszek

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Rosetta 3 - 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

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