This may be a really dumb question, but I am struggling to make sense of some data —so any input is welcome.
Hi everyone,
I apologize in advance if I am missing out on any critical detail that is relevant for troubleshooting this, but i'm completely new to trRosetta so please bear with me.
Currently, I am trying to run it with an MSA in order to construct an ab initio model for a target protein but I keep running into the following error
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core.scoring.hbonds.hbonds_geom: [ ERROR ] NAN occurred in H-bonding calculations!
Hey all! I am quite new to Rosetta and am using it for a project I am working on. My PI and I have found a paper in which we are wanting to use its code for minimizaiton and repacking but I really do not understand everything that is going on here. The code is as follows:
Hello,
I have a pdb with crystallographic waters which appear to be important for the protein structure, and perhaps function. I am generating mutations using pyrosetta and evaluting their relative scores, and exporting structures to be simulated with MD.
Currently to get the number of iterations a mover, such as FastRelax does, I enable the dump_trajectory scoretype and count the models in the PDBs (code below).
This seems very very weird way of doing this, so I was wondering if there is a less silly way of doing this?
Also, is there a direct way to open a multimodel file say to get the scores of each? (Rather than extracting the models, writing to file, reading them into PyRosetta and scoring them).
Hey all! I am quite new to Rosetta so I am hoping someone may be able to help. I understand how scoring works in Rosetta and how it is calculated but what I do not know is what a 'good' score is. I am trying to minimize a decently large protein and I don't know what sort of score I should be looking for. Thanks!
At the bottom of a scored PDB file is a POSE_ENERGIES_TABLE. The sum of total, which is already a dot product with the weights, does not match the total score.
Here is an example in Python3, either with or without PyRosetta —This is a question about the C++ not the Python bindinds, hence my posting in Rosetta General
Hello, I am new to using Rosetta so appologies for the very basic question
I work with Rosetta version 3.12 and I am following the tutorials: https://www.rosettacommons.org/demos/latest/Home
When I run the examples from the tutorials, the energy values I obtain are significantly different from the results of the tutorial.
We are using PyRosetta 2.83 to identify hydrogen bonds between atoms. For example, take the following code:
pose = pose_from_pdb("/Users/kmolloy/Downloads/2ezk.pdb")
hbond_set = pose.get_hbonds()
hbond_set.show(pose, 5)
hbond_set.show(pose,7)
This results of running this code are shown below:
