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Problem importing AlphaFold PDB

Submitted by Rick Neubig on Mon, 2023-01-09 09:48
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...".

 

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PyRosetta - 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

%time results = list(xml_obj(pose_obj)) error

Submitted by TENY BAEK on Wed, 2022-11-02 23:31
Category: 
PyRosetta

08.02-Ligand-Docking-pyrosetta.distributed.ipynb

When I ran the following syntax in this file, an error came out and it did not proceed.

if not os.getenv("DEBUG"):

    %time results = list(xml_obj(pose_obj))

I also set up Conda on Google Collabor
There is an error, do you know how to solve it?

The results of the implementation were as follows

 

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PyRosetta - Scripts

Install Error in Google Colab

Submitted by TENY BAEK on Sun, 2022-10-16 21:09
Category: 
PyRosetta

 

PyRosetta is being tested one by one in Google Collaboration. "01.02-PyRosetta-Google-Drive-Usage-Example.ipynb"

When I checked the file above while running it on Google Collabor, I got an error as below.

The previous 01.01 went well without errors, but the error comes out as below.
(version is PyRosetta4.MinSizeRel.python37.linux.release-332.tar. )

Please look down and give me your opinion.

- OS type :  Windows
- OS version : 10
- OS arch (32 or 64bit) : 64bit

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PyRosetta - Build/Install

"corrupted" small molecules. aromatic rings get distortet during relax

Submitted by patcD on Thu, 2022-07-21 04:51
Category: 
PyRosetta

Hello, i am trying to relax an enzyme with a co-factor (nadp) but whenever I do, the resulting structure looks wrong.

I use the NADP structure from pubchem as a starting point, then molfile2params structure  and copy paste the returned LG_0001.pdb to my protein. 

i then run the following code:

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PyRosetta - General

CONECT information for PDB files by raw sequence

Submitted by Fata on Wed, 2022-06-22 01:47
Category: 
PyRosetta

Hello,

I create a pose from sequence and dump it as PDB: 

pep_pose = pyrosetta.pose_from_sequence(sequence, res_type='fa_standard', auto_termini=True)
# pep_pose = pyrosetta.Pose()
# pyrosetta.rosetta.core.pose.make_pose_from_sequence(pep_pose, sequence, 'fa_standard', auto_termini=True)
pep_pose.dump_pdb(pdb_file_path)

As I understood, 'pose_from_sequence' creates a peptide structure by sequence, but what I found was that the PDB file misses the whole CONECT information.

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