# PyRosetta

## 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:

## 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?

Post Situation:

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

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

Post Situation:

## Install Error in Google Colab

Category:
PyRosetta

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. )

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

Post Situation:

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

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:

Post Situation:

Category:
PyRosetta

I have logged in Rosetta Commons.

But it seems that I have to log in at another website,

west.rosettacommon.org

I have used the same information here but it failed.

Post Situation:

## CONECT information for PDB files by raw sequence

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.

Post Situation: