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The above tells me that an RNA low-resolution potential
(rna_lowres_sf = core.scoring.ScoreFunctionFactory.create_score_function("rna/denovo/rna_lores_with_rnp_aug.wts"))
I am trying to use the makefragments.pl to get a sequence profile for 1203 residue monomer of the sars-cov-2 spike protein and Ive run into a error about SS0 predictor. Im using this command line
make_fragments.pl -verbose -psipredfile ab42c8a0-7d52-11eb-a871-00163e100d53.ss2 -n_frags 200 -n_candidates 200 -frag_sizes 3,9 sequence.fasta
I was wondering what things would make the predictor nonfunctional and if there is a physical file that I could interact with. Or if the predictor relies on files from the nr database.
when I do threading target sequence, and run the following command:
> $ROSETTA3/bin/partial_thread.default.linuxgccrelease -in:file:fasta 2_threading/1u19.fasta -in:file:alignment 1u19_2rh1.grishin -in:file:template_pdb 2rh1.pdb
I got the following result:
-bash: /bin/partial_thread.default.linuxgccrelease: No such file or directory
do I miss something?
For RNA, what kind of model can be defined as a centroid model?
Does rosetta have a function to generate a centroid model for RNA? For proteins, pose_from_sequence(sequence, 'centroid' ) can be used to generate a centroid model from the sequence. Is there a similar function for RNA?
I just installed Rosetta in my Mac and trying to do the ResettaCM following the tutorials (https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial). when i do the first step: Rosetta/demos/tutorials/rosetta_cm/scripts/clean_pdb.py 2RH1_ISOLATED A
I am new to MPI so please correct any misuse of terms. My question is about optimizing for MPI on an HPC or a second (preferred) solution to my issue is to optimize my RAM usage so I don't have to run MPI, serial would actually improve overall models produced anyways.