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I am trying to run code on https://github.com/strauchlab/scaffold_design
but it occur an error :
basic.io.database: [ WARNING ] Unable to locate database file scoring/score_functions/aa_composition/%%aa_comp%%.comp
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'startingstub_0000_0008_0001'
Error: [ ERROR ]
There are many energy terms in the output of the InterfaceAnalyzer, but is there any articles or other forms of materials which explain the basic principals or mathematical formats for calculating these energy terms in detail? And How rosetta codes for them? If I wished to add some energy terms in InterfaceAnalyzer, What is an effective way to learn the coding for this propose?
I will appreciate any help. With many thanks.
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
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:
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