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Silent File Scores Missing: RNA Protein Complex Predition

Submitted by axio23 on Fri, 2023-06-16 05:45
Category: 
Nucleic Acids

Dear Community,

I am relatively unexperienced with Rosetta and am for the first time trying to run the Protein RNA Complex Prediction Tutorial, as described on the website and the readme file using the latest weekly Ubuntu release. So apologies if I did a newcomer mistake.

When running as described, I get an error that I need to add the option base bair steps to false, so I added

-bps_moves false

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Rosetta 3 - Applications

Compilation and Setting up Rosetta

Submitted by Pj on Fri, 2023-06-09 21:38
Category: 
Compilation

Hello, I have had some problems with the compilation of Rosetta. I'm using Ubuntu 22.04.2 LTS. For compilation I used the release mode.

When I type: ./scons.py -j1 mode=release bin (OR) ./scons.py mode=release bin, I'm getting the following error:

 scons: Reading SConscript files ...

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Rosetta 3 - Build/Install

non-zero ddG of binding even without mutations

Submitted by top-gun98 on Wed, 2023-06-07 17:19
Category: 
Design

Hello,

I was trying to work with the "calculate protein-protein ddG" tutorial. The tutorial comes with a resfile for mutating an Alanine with Tryptophan at residue 98. Following the steps gives, I get a ddG value of -6.6533 REU.

However, when I replace the line "98 D PIKAA W" with "98 D PIKAA A" (i.e. esentially replacing the alanine with alanine), I'm still getting a ddG value of 6.6643 REU. Can anyone point out why I might be getting a non-zero ddG even though I'm not even 'mutating' the proteins.

Regards,

top-gun98

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Rosetta 3 - Applications

Scoring correlation with electron density map

Submitted by mrosam on Thu, 2023-05-25 05:14
Category: 
Structure prediction

I am trying to score how well different protein models fit into one electron desity map. I have tried using the score_jd2 tool with the flags:

"-database /programs/PDB/rosetta-3.13/main/database -in:file:s ./structures/*.pdb  -edensity:mapfile ./emd_12705.map -edensity:mapreso 3.6 -edensity::realign min -cryoem_scatterers true -grid_spacing 2.0 -fastdens_wt 35.0"

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Rosetta 3 - General

Changing amino acid profile while keeping the backbone conformation between 2 protein structures (need help)

Submitted by seamoon on Wed, 2023-05-24 07:46
Category: 
Design

Hello, i am a masters student trying to play around with rosetta. And i have a project in mind. I have two protein structures: nanocages. each with 60 monomers but the chains are a little bit different with different aa profiles. Now what I want to do is to make a structure with the backbone conformation profile of one of the nanocages but with the amino acid profile of the other one. How do i go about doing this? I'm sorry if I wasn't clear english is not my native language. 

Thanks for your help in advance. 

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Rosetta 3 - General

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