You are here

Unsolved

The problem hasn't been solved

READ THIS BEFORE YOU POST

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!

Post Situation: 

Academic email verification

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,

Post Situation: 

m6A modification on FARFAR2

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. 

Post Situation: 

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

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

Post Situation: 

Replacing a single residue in a structure

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.

Post Situation: 

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

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!

Post Situation: 

FixedBB design output no beta strands

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.

Post Situation: 

Predicting conformations of mutated residues

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!

Post Situation: 

Generating Params File for water molecule

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!"

Post Situation: 

Pages

Subscribe to RSS - Unsolved