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How to use base_pair_constraint for RNA as a constraint term？

Category:
Structure prediction

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"))

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What is an SS0 predictor?

Category:
Structure prediction

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.

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Ligand being read as part of protein structure

Category:
Docking

Hi,

I'm attemping a docking run with a protein that acts on an amino acid substrate. (tyrosine) Whenever I initiate the run it gives me the warning:

[ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 W TYS TYR:CtermProteinFull:NtermProteinFull:sulfated

core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CA .

And then the error:

[ ERROR ]: Caught exception:

File: src/core/pose/chains_util.cc:463

chain_id W does not exist

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Category:
Structure prediction

Hi folks,

when I do threading target sequence, and run the following command:

I got the following result:

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

do I miss something?

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Show I be using beta_nov16 scorefxn?

Category:
Scoring

ref2015 is the default at least in pyrosetta and is beta_july15 without the need for the boolean option correction:beta_july15 to be set.

In the cartesian ddG paper, Park et al. 2016, beta_nov16 is made, which has several difference (below, code used here).

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params file for beta-amino acids

Category:
Non-Canonical Peptides

Hi all,

I've been trying to insert a beta-amino acid into peptide, let's say, beta-homo-leucine. It seems that a params file for beta-hLeu is needed. Unforutnately, there is no params file for beta-hLeu in database in Rosetta, and molfile_to_params.py only works for alpha-amino acid. I've also visited https://rosie.rosettacommons.org/documentation/beta_peptide_design, but did't find helpful solution. So my question is:

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Protein Ensemble RosettaLigand Docking

Category:
Docking

Dear Rosetta Users,

I have an ensemble of protein conformations obtained by means of MD (Molecular Dynamics) simulation.
I would like to know if a recent protocol is available to dock one ligand to this protein ensemble using RosettaLigand.

Samuele

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Can rosetta generate a centroid model based on the rna sequence?

Category:
Structure prediction

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?

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