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Nucleic Acids

error running "helix_preassemble_setup.py"

Category: 
Nucleic Acids

Dear Rosetta users,

I recently install Rosetta and want to work with Rna_Denovo, when I run the command line below I got this error:

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Modelling temperature dependent RNA structures

Category: 
Structure prediction
Nucleic Acids

Hi to all,

I am really new to rosetta. I am using rna_denovo to generate 3D structures of RNA. I believe the default tempertaure used for modelling is 300K. I want to know if we can set our own temperature  for modelling RNA ? I did saw the option of temperature in the -help, written as 2 in the settings option, but I am not sure how to use it. Can we just define the temperature that we want, after writing this option? I am not sure how to go about this.

Please let me know the best way to go about this. And many thanks.

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Rna Denovo

Category: 
Nucleic Acids

Dear all,

Im using RNA Denovo rosetta protocol to build a 3D model of a small RNA segment (~10 nucleotides). For a specific purpose, i would like to model a ensemble of this ssRNA segment avoiding base pairing. I tried to modify some parameters but the ssRNA built is always packaged, with some base pairs. Is it possible to model such ssRNA using Rna Denovo protocol? 

 

Thanks in advance for any help!

Post Situation: 

DNA-protein docking

Category: 
Docking
Nucleic Acids

I didn't find any contemporary comment on that so I'd like to ask about how to dock protein structure to dsDNA in Rosetta? Is that possible now anyhow?

I have small protein structural motif, like HTH and try to model its interaction with a sequence within dsDNA to get some hints about which residues will bind to which DNA bases so I don't have to scan along huge DNA strands but rather have a well-defined location within the major groove to explore.

Thanks for all advice.

Post Situation: 

FARFAR2 error

Category: 
Structure prediction
Nucleic Acids
ROSIE

Hi ROSIE and FARFAR2 team,

       I used FARFAR2 to test the 3D structure prediction of several RNAs two weeks ago with native PDB uploaded. But all the jobs were finally dead with the error message "2-rescore_to_native_or_lowest". Could you tell me why this happened? You can find the sequence, 2D structure, and native PDB in the attachment.

Post Situation: 

Ligand question - aromatic bonds not being enforced?

Category: 
Constraints
Small Molecules
Nucleic Acids

Hi,

I am trying to run Local Relax on an ADP-bound protein structure. I cleared the first hurdle to make a ligand params file, and the program runs fine and includes the ligand. I made the params file by taking ADP from a related structure, converted it to mol2 using iBabel, and made the params file using molfile_to_params.py

Post Situation: 

Installing rna_denovo

Category: 
Nucleic Acids

Hi,

I tried using the Rosetta RNA tertiary structure modeling pipeline as described in your article "Modeling complex RNA tertiary folds with Rosetta."

My build is correct.

But every time I try to run

helix_preassemble_setup.py -secstruct sec.txt -fasta fasta.fasta

I am getting error as

Post Situation: 

Relaxing protein-RNA complexes

Category: 
Nucleic Acids

I'm new to Rosetta and I'm trying to relax a model of protein subunits bound to a short strand of RNA into cryo-EM density. However, I keep getting bad input errors on the RNA strand when I run this through relax and I would really appreciate some help. I have similar problems when I run the clean_pdb script which suggests to me that I'm not providing rosetta the correct instructions, the coordinates and residue names appear to be fine when inspected manually.

Thanks and Best wishes,

Rob

 

Post Situation: 

FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py

Category: 
Nucleic Acids

Dears,

After installing Rosetta 3.9 in a cluster and trying to run the simple command:

helix_preassemble_setup.py -fasta NFKB_1OOA_RNAStructure_2D.fasta -secstruct NFKB_1OOA_RNAStructure.secstruct

we get the following error:

Post Situation: 

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