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Mac build: cannot find main directory

Submitted by davidjaffe on Tue, 2022-05-17 11:44
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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Rosetta 3 - Build/Install

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

Submitted by ldlamini on Tue, 2022-05-17 02:37
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

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Rosetta 3 - Applications

RNA update library

Submitted by Anne Klein on Mon, 2022-05-16 16:04
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

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Rosetta 3 - General

Relax evaluates protein-DNA complexes?

Submitted by pablogalazdavison on Thu, 2022-05-12 12:05
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

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Rosetta 3 - Applications

-ignore_unrecognized_res doesn't work

Submitted by e3lm on Fri, 2022-05-06 14:47
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.

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Rosetta 3 - General

Is this the intended behaviour?

Submitted by Ken on Thu, 2022-05-05 14:59
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

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PyRosetta - General

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

Submitted by guowuchen on Thu, 2022-05-05 06:20
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:

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Rosetta 3 - General

Flex_ddG突变设计

Submitted by wangtao on Thu, 2022-05-05 02:46
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))

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