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Mac build: cannot find main directory

Category: 
Compilation

I am new to Rosetta.  I downloaded to my Mac and tried to build, following https://new.rosettacommons.org/docs/latest/getting_started/Getting-Started#introductory-rosetta-tutorials_installation-on-mac-linux.  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"

Category: 
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

Post Situation: 

RNA update library

Category: 
Nucleic Acids

Hi,

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/RNA_ChunkLibrary.cc line: 551

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job S_000001

[ ERROR ]: Caught exception:

File: src/core/import_pose/libraries/RNA_ChunkLibrary.cc:551

Post Situation: 

Relax evaluates protein-DNA complexes?

Category: 
Scoring

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.


Pablo

Post Situation: 

-ignore_unrecognized_res doesn't work

Category: 
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.

Post Situation: 

Is this the intended behaviour?

Category: 
PyRosetta

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) 

p.dump_pdb("test.pdb")

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

Best,

Ken

Post Situation: 

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

Category: 
Design

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

results:

Post Situation: 

Flex_ddG突变设计

Category: 
Design

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..../analyze_flex_ddG.py",line 215 ,in <module>

  analyze_output_folder(folder_to_analyze)

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

 ddg_score_dfs.append(apply_zemu_gam(ddg_scores))

Post Situation: 

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