Darwin Docs

BoltzGen - removed - external edit (Unknown date)

Anonymous (anonymous@undisclosed.example.com) — 2026-09-17T03:11:23+00:00

BoltzGen BoltzGen is installed in a shared conda environment (see usage here): conda activate boltzgen boltzgen run example/vanilla_protein/1g13prot.yaml \ --output workbench/test_run \ --protocol protein-anything \ --num_designs 10 \ --budget 2 # --num_designs is the number of intermediate designs. In practice you will want between 10,000 - 60,000 # --budget is how many designs should be in the final diversity optimized set

ESMFold2

v_sidorov (v_sidorov@undisclosed.example.com) — 2026-09-15T23:59:50+00:00

ESMFold2 ESMFold2 is installed in a conda environment (see usage Biohub/esm / model card). conda activate esm This points python at /opt/miniconda/envs/esm and sets HF_HOME to the shared offline cache (/mnt/scratch/esm/hf). Do not activate another conda env afterwards.

ColabFold - external edit

Anonymous (anonymous@undisclosed.example.com) — 2026-09-14T14:33:17+00:00

ColabFold LocalColabFold runs AlphaFold2 (and DeepFold) with cluster-local weights and MMseqs2 MSA databases. Usage: ColabFold / LocalColabFold. module load colabfold This puts colabfold_search / colabfold_batch on PATH and sets COLABFOLD_DATA to /mnt/scratch/colabfold

Known Issues

v_sidorov (v_sidorov@undisclosed.example.com) — 2026-09-14T13:55:06+00:00

Known Issues * The web-portal throws an error when a user logs in after waiting for too long on the login page. To overcome this, remove everything after “portal.darwin.bioeng.ru” in the address bar and reload the page. * nglview does not work if frontend (nglview inside the environment from which the JupyterLab starts) and backend (nglview inside the environment with the kernel the user is using) versions do not match. nglview inside user environments should always be 3.1.4 (except for cas…

Administration Guide - removed - external edit (Unknown date)

Anonymous (anonymous@undisclosed.example.com) — 2026-09-10T17:59:11+00:00

Administration Guide Backups * Configurations and overrides can be backed up in an encrypted way (see secrets.txt for the password) to Bioengineering Department NextCloud: dir=~/Documents/bioeng_data/darwin_assets assets=/root/assets ssh darwin_root " mkdir -p '$assets' tar -czpf '$assets'/ood.tar.gz \ /var/www/ood/public/custom.css \ /usr/share/ondemand-dex/web/themes/ondemand/styles.css \ /etc/ood/config/ondir=~/Documents/bioeng_data/darwin_assets assets=…

v_sidorov (v_sidorov@undisclosed.example.com) — 2026-09-10T17:38:10+00:00

Navigation * Home * Portal Guides * Basics * Advanced * Slurm * Migration from Newton * Application Guides * AlphaFold 3 * ColabFold * ESMFold2 * BoltzGen * Boltz2 * Hardware * Known Issues * Support

Boltz2

v_sidorov (v_sidorov@undisclosed.example.com) — 2026-09-10T17:31:44+00:00

Boltz2 Boltz2 is installed in a shared conda environment (see usage here): conda activate boltz2 boltz predict input_path --use_msa_server

cluster_ha.svg - created

localadmin (localadmin@undisclosed.example.com) — 2026-03-13T22:21:16+00:00