Error in H3_modeling_scores.fasc file from antibody_H3 program
Submitted by Brian Wiley on Sat, 2023-02-04 23:41
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Scoring
No values for total score while running Rosetta score file.
Submitted by Shweata Maurya on Wed, 2023-02-01 02:05
Category:
Scoring
I am running the Rosetta version - rosetta.source.release-334.tar.bz2 for designing two proteins but no values are generated for the total score. All the important files regarding this are attached. Please look at it and help me with this.
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Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi
Submitted by SamuelGong on Fri, 2023-01-27 06:20
Category:
Scoring
Hi,
using a flag containing options "-dunbrack_prob_buried_semi 0.8" and "-dunbrack_prob_nonburied_semi 0.8", errors appear like:
...................................
File: /home/shanghai/RationalDesign/Rosetta3.9/rosetta_src_2018.09.60072_bundle/main/source/src/utility/options/OptionCollection.cc:1314
Option matching -dunbrack_prob_buried_semi not found in command line top-level context
...................................
the flags and log file were attached.
Please help, thanks
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Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?
Submitted by JW_24 on Tue, 2023-01-24 04:40
Category:
Scoring
Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?
So far I thought the soft score function is supposed to feature lower repulsive terms.
ref2015_soft.wts:
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Calculating shape complementarity of ligand and protein
Submitted by varunmc99 on Tue, 2023-01-17 11:29
What should I do to lower down the fa_sol scores?
Submitted by JasonIsaac on Mon, 2022-12-05 18:57
Category:
Scoring
Greetings,
I ran a design protocol and I find my results score has high fa_sol scores like 250 around. What should I do to lower down the fa_sol scores?
I used ResidueSelector to separate my alpha-helixs into three parts: buried, semi-buried and solvent exposure. And use resfiles to assign the amino acids, buried------hydrophobic, semi-buried------less hydrophobic, solvent exposure-------hydrophilic.
And I am wondering if the fa_sol score of a model is too high, will it be insoluble in water after experimental expression?
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Score.sc file showing total score 0 for all protein structures created
Submitted by aanshi on Wed, 2022-11-23 11:13
Category:
Scoring
Hello, I am trying to use Rosetta to design the interface of my protein and would like to rank the predicted structures based on their scores however, after running the job, all the files show 0 for the total score. Could anyone take a look at my xml script and flags file (in the pdf file) to see if I'm missing something or how else to fix this issue? Thanks in advance!
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pose.energies().total_enegies().show_nonzero() changes after packer is applied
Submitted by Liviu Copoiu on Mon, 2022-11-07 16:51
Category:
Scoring
Hi, sorry to bother you I am using the following function to create a packer:
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Error with sequence_tolerance.R processing the checkpoint files, *.ga.entities and *.ga.generations.
Submitted by He Xiao on Mon, 2022-11-07 03:41
Category:
Scoring
Hello,
the output files, *.ga.entities and *.ga.generations, were produced by sequence_tolerance application.
When I tried to use sequence_tolerance.R processing the output files, I got the following error:
> source("/usr/local/rosetta_src_2021.16.61629_bundle/main/tools/analysis/apps/sequence_tolerance.R")
> process_seqtol("./2I0L_A_C_V2006_0001.ga.entities")
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total_score changes when decomposing bb hbonds ref2015
Submitted by Liviu Copoiu on Mon, 2022-10-31 15:40
Category:
Scoring
Hi. Really sorry to disturb you but I don't understand some behaviour regarding scoring.
I will first describe the issue and paste the code. Originally I was using
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