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cryptic error "Got some signal... It is:15" -- an issue with 'fixbb', or something else?

Category: 
Design

Hello Forum

I'm trying to run fixbb on my cluster here, and everything seems to have been going well for a while, but it suddenly stopped and spit out the following in the log file:

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Segment File Gen - no ouput

Category: 
Design

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. 

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Error with RosettaAntibodyDesign when running antibody_designer.linuxgccrelease

Category: 
Design

Dear friends,

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.

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protein surface design

Category: 
Design

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?

 

thank you!

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Do partner1 and partner2 in mover BackrubDD mean chain1 and chain2 respectively?

Category: 
Design

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

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problem parsing a THR residue

Category: 
Design

Hi all,

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:

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How does the label in pdb files looks like when using ResiduePDBInfoHasLabel?

Category: 
Design

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!

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Does it make sense if I do backrub after sequence design?

Category: 
Design

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.

Thank you!

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Rosetta job distribution error

Category: 
Design

Hi There,

 I am following rosetta protein design but every time I am getting job distribtion error message.  Here is output

 

<ROSETTASCRIPTS>

    <SCOREFXNS>
        <talaris_full weights=talaris2014>
            <Reweight scoretype="coordinate_constraint" weight=0.4/>
            <Reweight scoretype="res_type_constraint" weight=0.4/>
        </talaris_full>

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