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Nucleic Acids

building a protein-dna homology model via cm_rosetta

Submitted by y_atsmonraz on Wed, 2021-10-20 23:11
Category: 
Nucleic Acids

Hello everyone, recently I've been trying to make a homology model with a protein chain along with a nucleotide chain within it based on an existing template, but .

post-partial threading Rosetta dislocates the nucleotides nearly 1000 angstrom away from the structure. .

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Rosetta 3 - Applications

Stepwise error

Submitted by debostuti on Wed, 2021-10-06 08:57
Category: 
Nucleic Acids

I am getting the following error while trying to assemble a 514-nucleotide long RNA using the "Stepwise" programme:

"one of your input pdbs -- native, alignment, or starting -- has a residue that is not found in the fasta!"

I have thoroughly checked my target fasta sequence  and the input PDB containing part of the RNA structure. There are no residue mismatches...then why am I getting this error?

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ROSIE - General

duplex RNA

Submitted by amir_tagh on Thu, 2021-08-05 06:34
Category: 
Nucleic Acids

Hello,

I am using FARFAR to get the possible structures for a A-bulge RNA duplex with the following specifications:

Input sequence: CCGGCAGUGUG+CACACGUCGG

Input secstruct (((((.(((((+))))))))))

I need to keep the structure in the duplex form and not the hairpin. All output files I got with the mentioned specifications are RNA hairpins. Is there a way I can keep the structure in the duplex form.

 

thanks for yoyr help.

Best,

Amir

 

 

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Rosetta 3 - Applications

de novo RNA loop

Submitted by c.ocasion on Sun, 2021-02-14 18:34
Category: 
Nucleic Acids

Hello, 
I'm using the rosetta rna de novo tool to generate a rna hairpin, I used the RNA_Denovo_with_base_pair_steps demo as a guide to do it, however I get the error: Atom C1' 1 not found. I' m newbie using rosetta so I would really appreciate any help or guide about the problem. Thank you!

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Rosetta 3 - General

rna_denovo secstruct_general function

Submitted by rvandamme on Mon, 2021-02-01 13:39
Category: 
Nucleic Acids

Hello all, I had a question about how to properly use the -secstruct_general flag to input non-canonical and canonical basepairing interactions. I'm trying to test this on a simple structure from the 3IRW RNA that has a non-canonical g a basepair but I keep reseiving errors.  I am running the following command with the following files.

 

rna_denovo.static.linuxgccrelease -nstruct 1 -fasta ../test.fasta -secstruct_file ../test.secstruct -secstruct_general ../test.secgen -minimize_rna true -out:file:silent testing.out 

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Rosetta 3 - General

error running "helix_preassemble_setup.py"

Submitted by zahra_AZ on Tue, 2020-11-03 01:54
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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Rosetta 3 - General

Modelling temperature dependent RNA structures

Submitted by tuleshwori on Tue, 2020-05-19 01:16
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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Rosetta 3 - Applications

Rna Denovo

Submitted by helderveras on Wed, 2020-05-06 08:40
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!

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Rosetta 3 - Applications

DNA-protein docking

Submitted by ksteczk on Sat, 2020-04-11 11:23
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.

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Rosetta 3 - Applications

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