User contributions for Kholland
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8 October 2026
- 06:0006:00, 8 October 2026 diff hist +5 m Building and Docking on Cluster 7 No edit summary current
- 05:5905:59, 8 October 2026 diff hist −20 m Building and Docking on Cluster 7 No edit summary
2 October 2026
- 21:3421:34, 2 October 2026 diff hist +1 m Running ChemSTEP on CoreHPC No edit summary current
- 21:3421:34, 2 October 2026 diff hist +32 m Transition to coreHPC No edit summary current
30 September 2026
- 20:3320:33, 30 September 2026 diff hist +6,853 N Running ChemSTEP on CoreHPC Created page with "== 1. Source Environment == <pre> source /mnt/fac/CX900007_DS1/soft/chemstep/env.sh </pre> == 2. Dock the Seed Set == Copy the <code>.sdi</code> file for the library you want to use into a directory containing your dockfiles: {| class="wikitable" ! Library !! Path |- | 22B || <code>cp -r /mnt/fac/CX900007_DS1/work/kholland/22B_seed_building/sdi ./sdi</code> |} Then dock the seed set: <pre> bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh </pre> == 3. Gather Scores f..."
21 September 2026
- 21:4921:49, 21 September 2026 diff hist 0 m Running ChemSTEP No edit summary current
- 21:4721:47, 21 September 2026 diff hist +14 Running ChemSTEP No edit summary
- 21:4521:45, 21 September 2026 diff hist +183 Running ChemSTEP No edit summary
- 21:2521:25, 21 September 2026 diff hist −17 m Building and Docking on CoreHPC No edit summary current Tag: Manual revert
- 21:1921:19, 21 September 2026 diff hist +17 m Building and Docking on CoreHPC No edit summary
16 September 2026
- 21:2121:21, 16 September 2026 diff hist −199 Building and Docking on CoreHPC No edit summary
- 20:5820:58, 16 September 2026 diff hist −81 m Building and Docking on CoreHPC No edit summary
15 September 2026
- 21:5621:56, 15 September 2026 diff hist −4 m Building and Docking on Cluster 7 No edit summary
- 21:5621:56, 15 September 2026 diff hist +1,353 N Building and Docking on Cluster 7 Created page with "== 3D Ligand Building == Source the DOCK environment: <syntaxhighlight lang="bash"> source /nfs/software/dock/versions/dock385/env.sh </syntaxhighlight> Submit the building pipeline (Apptainer container, SLURM scheduler): <syntaxhighlight lang="bash"> python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder [output_folder_name] --bundle_size [bundle_size] --scheduler slurm --container_software apptainer --container_path_or_name $DOCK_INSTA..."
10 September 2026
- 19:3819:38, 10 September 2026 diff hist +9 Building and Docking on CoreHPC No edit summary
- 19:2819:28, 10 September 2026 diff hist +303 Building and Docking on CoreHPC No edit summary
9 September 2026
- 18:0318:03, 9 September 2026 diff hist +76 m Running ChemSTEP No edit summary
- 16:5316:53, 9 September 2026 diff hist −7 m Building and Docking on CoreHPC No edit summary
8 September 2026
- 18:5918:59, 8 September 2026 diff hist −1 m Building and Docking on CoreHPC No edit summary
13 August 2026
- 15:5715:57, 13 August 2026 diff hist −5 m Building and Docking on CoreHPC No edit summary
12 August 2026
- 23:0223:02, 12 August 2026 diff hist +41 Building and Docking on CoreHPC No edit summary
- 23:0023:00, 12 August 2026 diff hist +398 m Building and Docking on CoreHPC No edit summary
- 20:5020:50, 12 August 2026 diff hist +605 N Building and Docking on CoreHPC Created page with "3D LIGAND BUILDING: source /home/remote/jirwin3/fac/katiesoft/DOCK3.8/env.sh python $DOCK_INSTALL_PATH/zinc22-3d/submit/submit_building_docker.py --output_folder output --bundle_size 5 --skip_name_check --schedule slurm --container_software apptainer --container_path_or_name $DOCK_INSTALL_PATH/building_pipeline_oss.sif 5HT2C_actives.smi sbatch building_array_job.sh find /path/to/building/output -maxdepth 2 -name "bundle.db2.tgz" > [sdi_file_name}.sdi DOCKING: in a..."
7 July 2026
- 17:2017:20, 7 July 2026 diff hist +11,120 N Running ChemSTEP with SymDOCK Created page with "last update: july7 2026 katie. ChemSTEP (Chemical Space Traversal and Exploration Procedure) is an open-source, transparent acceleration algorithm for molecular docking capable of dealing with virtual libraries of several trillion compounds. This wiki page is a guide for BKS lab members to run ChemSTEP on Wynton HPC, using a subset of ZINC (22B or 72B) or 13.3B library from Enamine REAL. At a high-level, ChemSTEP is an iterative process that identifies molecules from..." current
22 June 2026
- 18:4818:48, 22 June 2026 diff hist −8 m Running ChemSTEP No edit summary
- 18:4418:44, 22 June 2026 diff hist +22 m Running ChemSTEP No edit summary
- 18:4318:43, 22 June 2026 diff hist +228 Running ChemSTEP No edit summary
12 June 2026
- 20:5220:52, 12 June 2026 diff hist +232 Running ChemSTEP No edit summary
- 19:3919:39, 12 June 2026 diff hist −1 m Running ChemSTEP No edit summary
- 18:5218:52, 12 June 2026 diff hist +291 Running ChemSTEP No edit summary
- 18:4718:47, 12 June 2026 diff hist +4 m Running ChemSTEP No edit summary
10 June 2026
- 22:4122:41, 10 June 2026 diff hist +2 m Running ChemSTEP No edit summary
26 May 2026
- 20:5020:50, 26 May 2026 diff hist −30 m Running ChemSTEP No edit summary
7 May 2026
- 22:5422:54, 7 May 2026 diff hist 0 m Running ChemSTEP No edit summary
- 22:4922:49, 7 May 2026 diff hist +3 m Running ChemSTEP No edit summary
- 22:4422:44, 7 May 2026 diff hist +687 Running ChemSTEP No edit summary
16 March 2026
- 16:5316:53, 16 March 2026 diff hist −7,832 Running ChemSTEP No edit summary
9 February 2026
- 20:2920:29, 9 February 2026 diff hist +4 m Running ChemSTEP No edit summary
12 January 2026
- 22:4322:43, 12 January 2026 diff hist +24 m Running ChemSTEP No edit summary
16 December 2025
- 19:4119:41, 16 December 2025 diff hist 0 Running ChemSTEP No edit summary
- 19:3019:30, 16 December 2025 diff hist +4 m Running ChemSTEP No edit summary
- 19:2719:27, 16 December 2025 diff hist −120 Running ChemSTEP No edit summary
- 19:2619:26, 16 December 2025 diff hist +119 m Running ChemSTEP No edit summary
15 December 2025
- 22:0622:06, 15 December 2025 diff hist +105 m Running ChemSTEP No edit summary
- 22:0422:04, 15 December 2025 diff hist −1,202 m Running ChemSTEP No edit summary
- 21:5921:59, 15 December 2025 diff hist +80 m Running ChemSTEP No edit summary
- 21:4021:40, 15 December 2025 diff hist +178 m Running ChemSTEP No edit summary
- 21:3921:39, 15 December 2025 diff hist +396 Running ChemSTEP No edit summary
- 21:1521:15, 15 December 2025 diff hist −73 m Running ChemSTEP No edit summary
- 20:5220:52, 15 December 2025 diff hist 0 m Running ChemSTEP No edit summary