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Nucleic Acids

Relaxing protein-RNA complexes

Submitted by rkirchdo on Fri, 2018-08-03 08:50
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

 

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Rosetta 3 - Applications

FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py

Submitted by obdulia on Wed, 2018-04-18 00:45
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:

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Rosetta 3 - General

Errors in Getting Erraser to run

Submitted by belousoff on Thu, 2017-06-01 16:13
Category: 
Nucleic Acids

Hey there,

I'm having trouble getting erraser to run. The following command:

erraser.py -pdb model_real_space_refined.pdb -map ../maps/FFT_13/70S_converted_1.ccp4 -map_reso 3.73

Give the errors as seen in the attached output.txt.

Everything compiled fine, using gcc5.4

any help would be appreciated.

 

cheers

 

matt B

 

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Rosetta 3 - Applications

constraints

Submitted by lah435 on Sun, 2017-03-12 03:25
Category: 
Nucleic Acids

My pose has DNA strands and I am trying to constrain the blunt ends.

Each DNA chain is numbered starting from 1. Why can't Rosetta find the atoms?

Here is my constraint:

AtomPair C1* 1C  C1* 35D  HARMONIC 12.028 1.00

And here is the error:

[ERROR] Exception caught by JobDistributor for job VGK8_v2_0001Atom 'C1* 1359' not found

 

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Rosetta 3 - General

calculate RMSD (RNA modelling)

Submitted by obdulia on Tue, 2016-07-05 01:58
Category: 
Nucleic Acids

Dears

With RNA modelling in Rosetta, how may i get the RMSD to a native structure for the whole set of generated models? I forgot to run the rna_denovo.linuxgccrelease with the -native flag and now, i would like to measure the RMSD for the obtained models (.out file) agaisnt the crystallographic structure.

Thanks a lot in advance

Best Regards

Obdulia

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Rosetta 3 - General

No RMS and IRMS values in protein/nucleic acid docking

Submitted by rbeier1 on Wed, 2016-01-13 12:41
Category: 
Docking
Scoring
Nucleic Acids

Hello,

I am docking a small protein / nucleic acid structure to generate dockings. The scoring contains only -nan for rms and 0.000 for Irms. Why doesn't the docking result in valid rms/irms values? Fnat and I_sc as well as total_score seem ok. What do I have to change in order to receive rms and irms values?

XML Rosetta Script (prot2.xml):

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Rosetta 3 - General

Re: Protein-RNA interface design

Submitted by bharat_46010 on Tue, 2015-04-07 04:44
Category: 
Design
Nucleic Acids

Hi,

I am trying to run the protein-RNA interface design protocol present in rosetta_demos. I found that in the xml file the residues that are allowed for design are not present in the protein (1a9n_ABQ). Am I missing something here ??

I also want to know whether rosetta can score protein-RNA interactions well or not, and what extra terms are scored in calculating the binding energy of the designed interface in case of protein-RNA interactions?

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Rosetta 3 - General

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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