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Submitted by Sergey on Thu, 2011-02-03 09:58

When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

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PyRosetta - Build/Install

NMR NOE based structure prediction

Submitted by Pooja on Sun, 2023-09-24 23:39
Category: 
PyRosetta

Based on the NMR NOE data, I want to use PyRosetta for the structure prediction of my peptides having unnatural amino acids. I went through the manual but couldn't find much information for structure prediction based on NMR data. It would be of great help if you cite protocols, scripts or literature used to determine the structure using NMR data in PyRosetta.

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PyRosetta - Applications

Academic email verification

Submitted by victor-calatayud on Mon, 2023-09-18 10:43
Category: 
ROSIE

Good afternoon,

I am a student at IPSI (Institució Pedagògica Sant Isidor) in Barcelona and I am currently looking forward to use Rosettadock. However, my email is not recognised as an academic one. My email is victor.calatayud.07@ipsi.cat, the domain being ipsi.cat. If you could verify it I would be very grateful. 

Thanks

Víctor Calatayud,

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ROSIE - General

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

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