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m6A modification on FARFAR2

Submitted by uke on Mon, 2023-09-18 04:31
Category: 
ROSIE

Hi everyone,

I been trying to work with FARFAR2 and I found documentation Fasta File (rosettacommons.org), which talks about possibilities of modified nucleotides on our RNA model; however, I could not find anything about m6A modification. I feel like there must be something for m6A given that it is most prevalent modification on RNA. 

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ROSIE - General

Altered pLDDT scores after running FastRelax on AlphaFold Multimer output pdb files

Submitted by franz72 on Sun, 2023-09-17 14:08
Category: 
PyRosetta

Hello,

I hope this message finds you well. I noticed after running FastRelax on output pdb files from AlphaFold Multimer that the pLDDT scores encoded in the B-factor fields have been altered. Is there a way to avoid this and maintain the original pLDDT scores? I have attached the code I am running below. 

Thank you,

Franz

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PyRosetta - Applications

Replacing a single residue in a structure

Submitted by Wexter300 on Sat, 2023-09-16 14:23
Category: 
Design

I have a structure i have been working with for a while, and I wish to replace the last residue in the sequence with a cysteine. I have tried to write a xml script that would perform the spot mutation, but I could not figure it out. Is there a specific rosetta function or way to perform spot mutations? I have also considered just manually replacing the residue with cysteine, and relaxing the structure through rosetta, but i'm not sure if the cysteine would stay in the sequence.

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Rosetta 3 - General

Dock cyclic peptide with non-canonical amino acids to protein target using rosetta flexpepdock?

Submitted by lei on Mon, 2023-09-11 23:34
Category: 
Docking

Dear Rosetta users,

Is it possible that we could use Rosetta flexpepdock to dock a cyclic peptide (backbone cycle, disulfide cycle, or chemical linker cycle) with non-canonical amino acids to protein target?

It seems we could model the structures for such cyclic peptide with non-canonical amino acids using Rosetta, but I am not sure their docking methods.

If not, could you please recommend a docking program in Rosetta or other software for this application?

Thanks!

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Rosetta 3 - Applications

FixedBB design output no beta strands

Submitted by tkoh on Fri, 2023-08-25 01:02
Category: 
Design

I am attempting to use the rosetta FixedBB design application to investigate possible conformation changes that may occur given a single point mutation whilst taking into account romaters. However, as an initial run of the application I do not change any residues or rotamers as I just want to see how this application works, but the resulting output differs from the input structure in that the beta sheets are not visible when visualized.

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Rosetta 3 - Applications

Predicting conformations of mutated residues

Submitted by Delfosse57 on Tue, 2023-08-22 12:26
Category: 
Structure prediction

Hi all,

I am attempting to predict the conformations of an enzyme after a single mutation. I have been using pymol to place the mutation into the protein and then I use the rosetta relax application to optimize the structure. Is this a valid way of performing this technique? Or should I be using rosetta scripts and repack the sidechains instead. I am worried that the relax protocol may not be able to optimize the residue if pymol puts it in a conformation that is far away from the optimal conformation.

Thank you!

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Rosetta 3 - General

Generating Params File for water molecule

Submitted by Ahmed Raslan on Thu, 2023-08-17 13:13
Category: 
Docking

Greetings,

I'm new to Rosetta, and I'm currently attempting to create a params file for docking water as a secondary ligand in my docking experiment. I'm using the following Rosetta script for this purpose:

Rosetta/main/source/scripts/python/public/molfile_to_params.py -n X00 -pX00 --conformers-in-one-file 0001H2O.mol2 --keep-names --chain D

However, I'm encountering an error message that reads: "ValueError: No acceptable neighbor atoms in molecule!"

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Rosetta 3 - General

Error when using published constraints file

Submitted by Delfosse57 on Thu, 2023-08-17 11:22
Category: 
Design

Hello,

I am attempting to follow a recent publication released by the Baker group. I am using this cst file to constrain an iron atom to a histidine:

https://github.com/ikalvet/heme_binder_design/blob/main/theozyme/HMM/HMM_His.cst

I have renamed the HMM residue to match with my ligand name.

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Rosetta 3 - General

ValueError("Path %s does not exist!" % path_name) for rna_helix.py

Submitted by kameisel on Wed, 2023-08-16 00:39
Category: 
Structure prediction
Nucleic Acids

Hi everyone,

I want to model helices with rna_helix.py but I get an error that rna_helix.linuxgccrelease isn't in the path where python script is looking for it:

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/rna_helix.py", line 27, in <module>

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