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Mac build: cannot find main directory


I am new to Rosetta.  I downloaded to my Mac and tried to build, following  This says that there should be a directory main/source, however I don't have it:

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Disulfidize- "Extra content at the end of the document"

Enzyme Design

Hello all!

I'm attempting (my first attempt) to use the disulfidize mover to predict disulfide bridges across a monomer of of homo-oligomer, this is the exact example on the tutorial.

I get this error "Extra content at the end of the document". I have run the the XML rewriter script on my .xml file  and there appears to be no issues.

I've attached my script. I'l appreciate any insight.

Thanks in advance

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RNA update library

Nucleic Acids


I'm building RNA structures of 4kb using rna_denovo. For some of my structures I have this error message: 

ERROR: hey update AtomLevelDomainMap & RNA_ChunkLibrary to not use magic numbers like 999 and 1000

ERROR:: Exit from: src/core/import_pose/libraries/ line: 551

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job S_000001

[ ERROR ]: Caught exception:

File: src/core/import_pose/libraries/

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Relax evaluates protein-DNA complexes?


Dear users,

I'm currently working on generating a DNA complexed protein and I thought I could use the relax application to avoid steric clashes generated during the "copy/paste" approach I used to put the DNA and protein together (after alignment with previously solved structure).

Does anybody have experience with improving the quality of DNA-protein complexes through Rosetta? my aim is to prepare the PDB for conventional molecular dynamics.

Any help is appreciated.


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-ignore_unrecognized_res doesn't work

Small Molecules

Hi, I'm minimizing structures in a list of PDB's using the -l option. Some structures have different ligands which I'd like to ignore or skip. The -ignore_unrecognized_res doesn't work. Minimize got bumped out trying to fill in missing atoms. Apparently it did not see or understand the flag.

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Is this the intended behaviour?


Hi all,

I am a new PyRosetta user and am running into something weird.  I am playing with some tutorial examples to get my feet wet and here is a very simple question.  When I do the following,

p = pose_from_sequence("Q"*5) 


I get the the side chain carbonyl oxygen bonded to the backbone (see attached pdb).  Is this the intended behaviour?



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RifGen error on rosetta, "assertion failed", please help!


Hi, everyone, sorry for disturbing! I ran into a error when I ran rifgen program to generate RIF residues for Patchdock.

commands line: $RIFDOCK/build/apps/rosetta/rifgen @input/rifgen.flag > rifgen.log 2>&1


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Hi all:
I am using flex_ddG to enhance interface binding by mutating an amino acid on a small peptide, running rosetta gives me results, but when I run the analysis python script to try to analyze the results I get an error as follows.
Problem Description。

File" /home..../",line 215 ,in <module>


File " /home/..../",line 194,in analyze_output_folder


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