You are here

Unsolved

The problem hasn't been solved

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

Post Situation: 

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

Post Situation: 

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!

 

Post Situation: 

How to use base_pair_constraint for RNA as a constraint term?

Category: 
Structure prediction

https://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb

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"))

Post Situation: 

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.

Post Situation: 

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

Post Situation: 

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?

Post Situation: 

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).

Post Situation: 

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:

Post Situation: 

Pages

Subscribe to RSS - Unsolved