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Scoring

ERROR: Unable to open weights/patch file

Category: 
Scoring

Hello,

I am getting the following error:

ERROR: Unable to open weights/patch file. None of (./)ref2015 or (./)ref2015.wts or /cluster/rosetta/bin/mpi/../database/scoring/weights/ref2015 or /cluster/rosetta/bin/mpi/../database/scoring/weights/ref2015.wts exist

Post Situation: 

Per residue total score

Category: 
Scoring

Hi Rosetta Team!

I read from the scoring tutorial this line

A rule of thumb: -1 to -3 REU per residue is typical while scoring a refined structure with ref2015 score function.

May I know if it is possible to directly call this per residue total score during scoring?

Thank you.

Post Situation: 

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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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

Post Situation: 

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: 

InterfaceDdGMover and ResfileReader

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

Post Situation: 

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