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When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

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- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation: 

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

Post Situation: 

Adding positional restraints to pure RNA system in DRRAFTER and rna_denovo

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

Post Situation: 

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:

Post Situation: 

Structure prediction using true distance and angle constraint

Category: 
Structure prediction

Hello,

I wonder if naive protein structure can be predicted by using true distance and angle constraints.
If we can do that, how do we choose rosetta applications and parameters?

Post Situation: 

antibody protocol fails

Category: 
Structure prediction

Hello,

I'm using antibody protocl to graft some models but it fails with the following error:

File: src/protocols/antibody/grafting/chothia_numberer.cc:152
ERROR: Unxpected length of light-fr3 [length=31], length expected to be: [32, 33, 34]!

Do you have any comments on this? I have three sequences (three different antibodies with light and heavy chains) and it works on one of them but the same error on the two others.

Thanks a lot in advance,

Best

Post Situation: 

debug rosetta_scripts FunFolDes run

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 

Post Situation: 

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