# Scoring

## Output and Input Tutorial

Category:
Scoring

After I had moved to the input_file directory following the Controlling Input and Output in Rosetta,I ran,

\$ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb

and I got the output,

-bash: /bin/score_jd2.default.linuxgccrelease: No such file or directory.

What would you recommend doing?

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## Antibody scoring

Category:
Scoring
ROSIE

Hi,

I am wondering what the scores that are provided in the score file of an antibody job mean. Does a more negative score mean that a model is expected to be closer to the native structure?

Thanks!

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## ShapeSimilarity, ElectrostaticSimilarity (RosettaSurf)

Category:
Scoring

Hi all,

I would like to try out ShapeSimilarity and ElectrostaticSimilarity filters that were described in the 3.13 release notes (https://www.rosettacommons.org/docs/latest/release-notes), but the links on that page says it's "Forbidden. This Wiki is set to no-edit mode."  I tried adding it to Rosetta script and I get "This element is not expected" error.  Would somebody be able to point me to the right direction?

Best,

Ken

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## Relax evaluates protein-DNA complexes?

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

Post Situation:

Category:
Scoring

Dear all,

I have two issues with Rosetta and I would really appreciate your help.

The first one is in InterfaceDdGMover

"In InterfaceDdGMover, there are no valid chains to translate when unbinding!"

The second one on another system is in ResfileReader:
"On line 3, the pose does not have residue with chain=B, PDBnum=417."

Thank you very much,

Best regards,

Asaf

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## Differentiable Energy Function w/ Centroid Representation

Category:
Scoring

Hi!

I have a protein complex that's represented in terms of the sequence, the pairwise distances between the CA atoms, and the phi and psi dihedral angles. These distances and dihedral angles should be reasonably correct. I do not have access to the coordinates (N,CA,C,O, etc.) of this protein complex.

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## Modelling at defined pH - for pmutscan - pH:mode not working

Category:
Scoring
Loop Modeling
Chemically Modified Residues

Hi all,

I am new to Rosetta and using various Rosetta protocols, primarily remodel and pmutscan, to assess the impact of various mutations on protein stability. I would like to model the protein and associated mutations at acidic pH as this may affect salt bridge formation and overall REU score.

Post Situation: