Hi,
I'm just wondering, is the CASP local Distance Difference Test implemented in Rosetta?
Hello!
I am trying to find the residues interacting with a particular residue of interest so as I can determine which residue-residue interaction is making the most contribution to a specific scoring term. However, I have not been able to find the residue_pair_energy function.
Do I need to write the function class to obtain this or is there a function that already available (e.g. to get atom-atom pairwise energies). If the latter case where is the function located.
I have tried core.scoring.Energies but it does not exist there
I'm using "rosetta_src_2017.36.59679_bundle". I'm trying to run the following bash script:
#!/bin/bash
$ROSETTA3/home/labusr/rosetta/main/source/bin/score_jd2.macosclangrelease \
-database $ROSETTA3/database/ \
-database ~/Rosetta/database/ \
-in::file::s /home/labusr/Documents/1issA.pdb \
-ignore_unrecognized_res \
-edensity::mapfile /home/labusr/Documents/1issA_6A.mrc \
-edensity::mapreso 5.0 \
-edensity::grid_spacing 2.0 \
-edensity::fastdens_wt 35.0 \
-beta \
-edensity::cryoem_scatterers \
-crystal_refine
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!
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
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:
Hi,
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?
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?
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.
