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

Submitted by johnnytam100 on Fri, 2019-08-23 21:10
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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Rosetta 3 - Applications

problem parsing a THR residue

Submitted by decrSTL on Wed, 2019-08-21 12:25
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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Rosetta 3 - General

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

Submitted by johnnytam100 on Fri, 2019-08-16 00:25
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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Rosetta 3 - Applications

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

Submitted by johnnytam100 on Thu, 2019-08-15 05:15
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 3 - Applications

Rosetta job distribution error

Submitted by ss on Thu, 2019-08-01 09:26
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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Rosetta 3 - General

RosettaDesign

Submitted by ac.research on Sun, 2019-07-21 01:20
Category: 
Design

Hello Everyone,

I have been trying to find a solution to RosettaDesign where it can reliably design proteins.

I have tried the following protocols: 

FIXBB with resfile   - faield
FIXBB                - faield
FLXBB with blueprint - failed
FLXBB                - failed
Remodel              - failed

In each protocol I choose the lowest scoring decoy from 100 generated decoys. I run an abinitio simulation (25,000 decoys) but I do not get a funnel shaped plot.

 

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Rosetta 3 - General

Mutations are ignored (fixbb) when using -auto_setup_metals option

Submitted by hdelrisco on Wed, 2019-06-19 15:43
Category: 
Design

When using fixbb.static.linuxgccrelease (2018 or 2019 release) with the -auto_setup_metals option set, see cmd line below, all mutations to a residue with a link to a metal ion, are ignored in the model generated (PDB file).

Run process: /usr/local/rosetta/main/source/bin/fixbb.static.linuxgccrelease -s ../src_updated_0001.pdb -extra_res_fa ../sub.params -resfile resfile-S100.txt -nstruct 1 -ex1 -ex2 -database /usr/local/rosetta/main/database -jran 1001 -constrain_relax_to_start_coords -use_input_sc -minimize_sidechains -overwrite -auto_setup_metals

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Rosetta 3 - General

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