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Is there a limitation of RNA length using farfar2?

Submitted by lwb on Wed, 2023-01-04 19:09
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!

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ROSIE - General

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

Submitted by johnnytam100 on Thu, 2022-12-15 00:23
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 

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PyRosetta - Build/Install

How to resolve the error about pyrosetta.distributed

Submitted by TENY BAEK on Tue, 2022-12-13 00:45
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.

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PyRosetta - Build/Install

Unexpected length of light chain FR1

Submitted by mgupta on Fri, 2022-12-09 01:03
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]!

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Rosetta 3 - General

Prepacking crashing using metalloprotein

Submitted by mb0261 on Tue, 2022-12-06 10:16
Category: 
Docking

Good evening, 

I'm trying to run an ensemble protein-protein docking to a protein containing a metal cluster (2Fe2S). I was able to generate ensembles for both structures, but at the Prepcking stage the application just crash. Here is the command:

$ docking_prepack_protocol.default.linuxgccrelease -in:file:s ../input/mnt_bcl2_relaxed.pdb -ensemble1 ../ensemble/mnt/mnt_A_ensemblelist -ensemble2 ../ensemble/bcl2/bcl2_B_ensemblelist -partners A_B -in:auto_setup_metals true @prepack_flag

Here is the error message:

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Rosetta 3 - General

What should I do to lower down the fa_sol scores?

Submitted by JasonIsaac on Mon, 2022-12-05 18:57
Category: 
Scoring

Greetings,

I ran a design protocol and I find my results score has high fa_sol scores like 250 around. What should I do to lower down the fa_sol scores? 

I used ResidueSelector to separate my alpha-helixs into three parts: buried, semi-buried and solvent exposure. And use resfiles to assign the amino acids, buried------hydrophobic, semi-buried------less hydrophobic, solvent exposure-------hydrophilic. 

And I am wondering if the fa_sol score of a model is too high, will it be insoluble in water after experimental expression?

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Rosetta 3 - General

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