How does one convert a PDB file of an antibody to AHO scheme?
Hi,
I'm receiving the following error message:
Hi,
I'm receiving the following error message:
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...".
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
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.
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
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
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:
I have logged in Rosetta Commons.
But it seems that I have to log in at another website,
west.rosettacommon.org
so what is the username and password?
I have used the same information here but it failed.
Hi,
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.