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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

Adding positional restraints to pure RNA system in DRRAFTER and rna_denovo

Submitted by zharmad on Fri, 2019-08-23 01:16
Category: 
Constraints

I'm running into some issues applying the DRRAFTER instructions to model RNA loops between several distinct rigid-body helices, and am asking for advice here on how to proceed.

My goal is to rebuild the loop structures between two base-paired regions opf a stem loop. A fake secondary structure is like so:

>...5'-strand-of-pieceA...stemloop...3'-strand-of-pieceA

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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

debug rosetta_scripts FunFolDes run

Submitted by tatsiana.bylund on Sun, 2019-08-18 23:17
Category: 
Compilation

I'm running a FunFolDes and it works for one protein, but outputs segmentation fault on other three. I checked all the proteins contain standard amino acids, no cys.

Admin installed debug version on our cluster and said to run ml rosetta/2019.14.debug, but i can't find anywhere how to run debug version.

i was running 

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Rosetta 3 - Applications

A problem with "make_fragments.pl" script dependencies

Submitted by Corvin on Fri, 2019-08-16 04:30
Category: 
Structure prediction

Dear fellows,

I would like to generate fragments for protein sequence structure prediction ab initio locally, on my laptop, without involving any server, such as Robetta. I carry out it with a help of make_fragments.pl script. And I met with several problems with make_fragment.pl dependencies. I want to solve these problems. Could you advise me, if you can, how to solve them, please?

My first problem consists in follows:

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Rosetta 3 - Applications

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

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