MWNautilus

jax.tree_util.tree_multimap() is deprecated

13

I got the follwoing messenge in cell 5 (run alphafold & relax with AMBER): /usr/local/lib/python3.7/dist-packages/jax/_src/tree_util.py:189: FutureWarning: jax.tree_util.tree_multimap() is deprecated. Please use jax.tree_util.tree_map() instead as a drop-in replacement. 'instead as a...

Installation procedure not working for Ubuntu 20.04 LTS

9

Following the installation procedure on the Bookworm website as follows sudo add-apt-repository ppa:bookworm-team/bookworm sudo apt-get update sudo apt-get install com.github.babluboy.bookworm just leads to an error message (some package termed "ninja"...

Request: pLDDT & pTMscore to be stored in downloaded results archive

3

I hope I haven't overlooked something but would it please be possible to store the pLDDT and pTMscore values in a file that would be added to the downloadable model...

Question: Issue with automated model ranking in mmseqs notebook?

3

Yesterdays protein modeling gave the following log output with regard to the ranking of the five generated models: `2023-09-22 18:52:35,633 alphafold2_ptm_model_1_seed_000 recycle=0 pLDDT=88.1 pTM=0.799 2023-09-22 18:54:13,264 alphafold2_ptm_model_1_seed_000 recycle=1 pLDDT=87.9 pTM=0.814...