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Structure Prediction of protein mutant using relax

Category: 
Structure prediction

Hello,

I am attempting to predict the structure of a metalloenzyme after 5 mutations using the relax function. My current protocol consists of adding the following:

- Adding a mutation to the protein in pymol

- Relaxing the protein and picking the lowest energy structure

- Adding another mutation to the lowest energy structure and repeating until all mutations have been added.

Post Situation: 

Problem importing AlphaFold PDB

Category: 
PyRosetta

I have tried to import a PDB that came from an AlphaFold Docking run. I have repaired it using the PRAS server to add the OXT lines (file attached) but it still won't import. Here is the script for import followed by the first lines of the results with the error messge "discarding 4 atoms at position 1 in...".

 

Post Situation: 

Access to Rosie via GitHub Authentication

Category: 
ROSIE

Dear colleagues.

Would you like to verify my academician e-mail for access to Rosie via GitHub Authentication?

My institution is Taras Shevchenko National University of Kyiv (Kyiv, Ukraine).

Our main academician domain is @knu.ua.  Our additional (old) domain is @univ.kiev.ua.

Sincerely

Alex Nyporko

Post Situation: 

Is there a limitation of RNA length using farfar2?

Category: 
Structure prediction

Hi, I recently used farfar2 to predict some RNA structures, but it seems that the longest RNA sequence that would succeed is beneath around 500-600 nt. When I submit sequences with 1800, 2000 or 7500 nt, they failed with returning "No output silent files were produced in the FARFAR2 step; please double-check your inputs!", and I couldn't figure out why. So I wonder is there a limitation of RNA length or size when using farfar2 to predict structures(which I've searched and not found yet), or I just made other mistakes somewhere else. Thanks a lot!

Post Situation: 

Installing PyRosetta on Jupyterlab notebook (i.e. not colab)

Category: 
PyRosetta

Hi Rosetta team.

I want to install PyRosetta on Jupyterlab notebook (i.e. not colab).

More specifically, the Jupyterlab notebook was spun up from a virtual machine (VM) on the Google Cloud Platform (GCP).

I tried to use ordinary installation commands from colab notebooks, that were

!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()

but didn't work, giving 

Post Situation: 

How to resolve the error about pyrosetta.distributed

Category: 
PyRosetta

Hello. I'm getting a lot of help from looking at the questions and answers here.

I'm learning it by running it one by one through pyrosetta notebook.

distributed_overview.ipynb

It says pyrosetta is not recognized when running in the conda environment with the above file, is there any way?

Also, the pyrosetta.distributed environment is not working well, so do you have a URL or guide to refer to?

Thank you in advance for your reply.

Post Situation: 

Unexpected length of light chain FR1

Category: 
Structure prediction

Hello Rosetta forum,

I recently started using rosetta for building antibody structures and running "antibody.linuxgccrelease -fasta L2251x0566aa.fasta | tee grafting.log" command on my sequences. Seems like the default setting doesn't prefer light-FR1 length >22 ? Any help would be appreciated.

File: src/protocols/antibody/grafting/chothia_numberer.cc:149
ERROR: Unxpected length of light-fr1 [length=23], length expected to be: [19, 20, 21, 22]!

Post Situation: 

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