# Unsolved

The problem hasn't been solved

## GeneralizedKIC loop closure error

Category:
Loop Modeling

Dear Rosetta Community,

I am trying to generate conformations for a 29 residue cyclic peptide with N-C terminal cyclisation. I've written a Rosetta Script that declares a bond between the N and C terminals and then performs a loop closure based on GeneralizedKIC.

However I am facing the following error:

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## Pyrosetta score protein structures with missing atoms in sidechain

Category:
PyRosetta

I have a question regarding Pyrosetta. Currently, I want to use pyrosetta to score some protein structures but with missing atoms in sidechain. So my protein structures contrain full-atoms for backbone but missing one or two atoms per residue on sidechain. I used pose_from_pdb to read my protein structure (pdb). But it seems pysoretta will fill in the missing atoms according to rotamer library. Is there a way to prevent it so I can just score my structures with missing atoms on sidechains?

Thanks a lot for the help,

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## Patch to impose tetrahedral geometry on backbone O atom

Category:
Non-Canonical Peptides

Hello,

I want to model the tetrahedral transition state of an enzyme where serine OG attacks the peptide backbone C atom. In this case the bond order of the backbone C=O bond changes to C-O(H) and the C-O(H) is not in plane anymore.

So far I wrote this patch file and added a hydrogen to the O atom in the input model which is named H01. The patch file is used since I get an error when I don't include it.

BEGIN_CASE

BEGIN_SELECTOR
NAME3 LEU
END_SELECTOR

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## Best way to store a pose by Pyrosetta for Pyrosetta

Category:
PyRosetta

A pose can have a constraint set, a modifiable residue set, an unnoticed pose.pdb_info().obsolete() == True case, virtual residues, energies and a few more. Therefore when saving to disk none of the following truly work as they save coordinates:

pose.dump_pdb('foo.pdb')
pose.dump_scored_pdb('foo.pdb', pyrosetta.get_fa_scorefxn())
pose.dump_cif('foo.cif')
pose.dump_mmtf('foo.mmtf')
pyrosetta.io.poses_to_silent([pose], 'foo.silent')

So I was hoping for an all-in-one

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## PDB Clustering

Category:
Scoring

Hello,

I was working on homology modeling and built 1000 models with ligands. I'm planning to select 100 top scored models and do clustering on them.

I tried cluster.linuxgccrelease, but the program didn't recognize the ligand. I specified the option -exclude_res, but it didn't work.

I also tried calibur.linuxgccrelease, but there are a lot of warnings instead of the output.

I'm attaching the log files. Can you help me with these issues? Thank you in advance!

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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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## Thread target sequence

Category:
Structure prediction

Hi folks,

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?

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