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I am in need of some major help.
I am running the SEWING application because I am copying the secondary structures that fit onto a particular primer, and some key binding residues are located on the loop between two beta strsnds - so I need to generate a new segment file with a few beta strands.
As a new learner of rosetta, I encountered an error "chain_id A represents more than one chain!" after I downloaded the 5ugy.pdb file from RCSB PDB database and renumbered to the AHo Scheme with PyIgClassify Server.
If anyone can help me with this issue? Any help would be appreciated.
I'm running FunFolDes on a template and the generated models have very hydrophobic surfaces. They used human-guided design to introduce charged/hydrophilic mutations on the surface. Is there an automatated way to favor charged/hydrophobic mutations on the surface to begin with?
has anyone used https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/AACompositionEnergy for this purpose?
I was doing the design of a protein interface. The starting structure was two chains in contact with each other.
Previously I have tested turning on and off partner1 and partner 2 of BackrubDD, so what I understood from the design behavior was:
partner1="0" -> no flexible design of chain 1 backbone
partner1="1" -> with flexible design of chain 1 backbone
partner2="0" -> no flexible design of chain 2 backbone
partner2="1" -> with flexible design of chain 2 backbone
I've a problem that has been stumping me for days, I have a peptide structure that I pulled from a MD trajectory. I'm unable to get any Rosetta modules like relax, or fixbb to work with this structure, the jobs always start off fine but as soon as they hit a THR residue of which there are four I get the following:
core.chemical.ResidueType: [ ERROR ] atom name : CZH not available in residue THR
I see nothing wrong in my PDB file, here's the first THR residue:
I want to use ResiduePDBInfoHasLabel to select a subset of residues.
However, I could not find an example pdb that shows me how the residues are labeled (i.e. the format of labelling in pdb).
May I have an example from anyone who has used ResiduePDBInfoHasLabel before?
Thank you very much!
Hi all, just a very simple question that I want to have your opinion:
Usually, we do sequence design after backrub (i.e. flexible backbone sampling).
Does it make sense if I do backrub after sequence design?
Just curious how will it be different, with an opposite order.
i'm running FunFolDes .
but want to rewrite it for new scoring function and new BUNS.
I am following rosetta protein design but every time I am getting job distribtion error message. Here is output
<Reweight scoretype="coordinate_constraint" weight=0.4/>
<Reweight scoretype="res_type_constraint" weight=0.4/>