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I have a protein complex that's represented in terms of the sequence, the pairwise distances between the CA atoms, and the phi and psi dihedral angles. These distances and dihedral angles should be reasonably correct. I do not have access to the coordinates (N,CA,C,O, etc.) of this protein complex.
I am new to Rosetta and using various Rosetta protocols, primarily remodel and pmutscan, to assess the impact of various mutations on protein stability. I would like to model the protein and associated mutations at acidic pH as this may affect salt bridge formation and overall REU score.
Hello, I would like to use or be able to visualize in the score file some terms or information related to docking and similar protocols, for example, interface_score and rms in other scoring functions executing other movers. Can this be done with flags? I hope you can help me, thanks.
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.