Request for access to PyRosetta 3 for DeepAccNet refinement

[sameknovaes]

I am modeling the 3D structures of some proteins and need to refine them using DeepAccNet. However, DeepAccNet requires PyRosetta 3, and I have been unable to find any available version of PyRosetta 3 online. Would it be possible to provide access to, or upload, a version of PyRosetta 3 so that I can proceed with the installation?

Thank you very much for your time and assistance!

[lyskov]

Hm… the last release of PyRosetta-3 was from ~10 years so I am a bit skeptical that it was used in "DeepAccNet refinement" (I am assuming you referring to https://www.nature.com/articles/s41467-021-21511-x) . So it seems the most likely is that authors of DeepAccNet actually meant PyRosetta-4. Have you tried using one of the latest PyRosetta-4 builds to see if it works? Also do you have a concrete release number for that PyRosetta? Thanks,

[sameknovaes]

I couldn’t find the exact PyRosetta release number they used. I was a bit skeptical about them using PyRosetta 3 too, but the README file in the modeling directory (https://github.com/hiranumn/DeepAccNet/tree/main/modeling) lists PyRosetta 3 as one of the required libraries. When I try to run DeepAccNet, I get this:

python DeepAccNet.py samples outputs

┌───────────────────────────────────────────────────────────────────────────────┐

│                                  PyRosetta-4                                  │

│               Created in JHU by Sergey Lyskov and PyRosetta Team              │

│               (C) Copyright Rosetta Commons Member Institutions               │

│                                                                               │

│ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRES PURCHASE OF A LICENSE │

│          See LICENSE.PyRosetta.md or email license@uw.edu for details         │

└───────────────────────────────────────────────────────────────────────────────┘

PyRosetta-4 2025 [Rosetta PyRosetta4.Release.python37.ubuntu 2025.41+release.de3cc17d509259e29147a2ed8f2a726d644e7e34 2025-10-06T16:25:46] retrieved from: http://www.pyrosetta.org
# samples: 18
Featurizing 18 samples. 0 are re-processed.
While processing outputs/ACE_P12821_S660C.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/ACE_P12821_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/AGTR1_P30556_I103T.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/AGTR1_P30556_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/ANPEP_P15144_R381L.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/ANPEP_P15144_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/CMA1_P23946_MT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/CMA1_P23946_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/CPM_P14384_R24S.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/CPM_P14384_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/CPN1_P15169_G217E.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/CPN1_P15169_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/LNPEP_Q9UIQ6_I630R.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/LNPEP_Q9UIQ6_N948Y.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/LNPEP_Q9UIQ6_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/MAS1_P04201_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/XPNPEP2_O43895_G151V.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
While processing outputs/XPNPEP2_O43895_WT.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'