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• 21:53, 18 March 2024 Khtang talk contribs created page Renew Schrodinger Licenses (Created page with "'''<big>Cluster 0 and 2 licenses are expired on March 15th annually. </br> Contact licensing@schrodinger.com (CC John and Brian) and tell them that you are from Shoichet Lab and would like to renew TWO licenses. They will send the Cluster 0 license to John and Cluster 2 license to Brian</big>''' === Get License File === Get the email about Schrodinger license keys ready for retrieval from John or Brian.</br> Click the link that said '''please user this form to generate...")
• 21:26, 22 February 2024 Frodo talk contribs created page How to release DOCK (asdf) Tag: New redirect
• 21:26, 22 February 2024 Frodo talk contribs deleted page How to release DOCK (content was: "To release DOCK: * log in as root to dock.compbio.ucsf.edu aka bksmailman. e.g. from gimel2. * bksmailman is canonical, and pw is based on c2 * cd to /var/www/html/distributions * the active version of dock 3.8 is dock.3.8_source.tar.gz which currently points to pydock3-1.0.0.tar.gz * suggest you upload as pydock3-1.1.0.tar.gz and point dock.3.8_source.tar.gz * tell John you have...", and the only contributor was "Frodo" (talk))
• 21:04, 22 February 2024 Frodo talk contribs created page Create venv (shoulda had this a long time ago)
• 00:05, 22 February 2024 Khtang talk contribs deleted page Notes from first attempt at globus (content was: "https://www.globus.org/globus-connect-server In an attempt to install Globus Connect Server, here is my notes of what I have done so far. Note: I have tried installed Globus on gimel2, tau. So far no luck getting it working Detail complete guide https://docs.globus.org/globus-connect-server-installation-guide/ https://www.h3abionet.org/images/Technical_guides/L2_04_How_To_Setup_and_Configure_Globus_Connect_Endpoint_V1.5.pdf === Open required TCP Ports === ==== Check if FQ...")
• 22:15, 20 February 2024 Mtsukanov talk contribs created page Covalent Library Preparation 2024 (Created page with "Modify warhead to covalent adduct with SiH3 added. == Prepare “SMILES ID” file. == ssh n-1-17 (or another development node) Source environment with RDkit source /mnt/nfs/ex9/work/ttummino/miniconda/etc/profile.d/conda.sh conda activate base3.7 python ~ak87/PROGRAM/convert_smiles_to_covalent.py ald bbv-cov-ald.smi bbv-cov-ald-test.smi This script enumerates all stereoisomers and converts SMILES to the covalent ones. Currently, only conversions for aldehydes...")
• 22:20, 15 February 2024 Khtang talk contribs moved page Schrodinger notes to Schrodinger
• 21:11, 13 February 2024 Khtang talk contribs created page MediaWiki:Sidebar (Created page with " * navigation ** [https://calendar.google.com/calendar/u/6/embed?src=90hc5i060oggekk2s3c8sluf4g@group.calendar.google.com&pvttk=b015223b9cc576dce92e6cc7698935cd&csspa=1 BKS Calendar] ** mainpage|mainpage-description ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|help-mediawiki * SEARCH * TOOLBOX * LANGUAGES")
• 21:08, 13 February 2024 Khtang talk contribs changed group membership for Bks.labmanager from (none) to interface administrator
• 20:44, 13 February 2024 Khtang talk contribs blocked 小千代我老婆 talk contribs with an expiration time of indefinite (account creation disabled)
• 20:11, 9 February 2024 Ianscottknight talk contribs created page Calculate ECFP4 using RDKit (Created page with "1. git clone https://github.com/docking-org/ChemInfTools.git 2. Ensure that you have sourced a python3 environment E.g., source /nfs/soft/ian/python3.8.5.sh 3. python ChemInfTools/utils/teb_chemaxon_cheminf_tools/generate_chemaxon_fingerprints_py3.py <SMILES_FILE> <OUTFILE_PREFIX>")
• 18:50, 29 November 2023 Jgutierrez6 talk contribs created page Globus Curator's Guide (Created page with "== Introduction == Here will be instructions on how to maintain globus == Updating Path Permissions == 1. Identify the real paths of the permission denied paths. Globus doesn't follow symbolic links <source>readlink -f <symlink> </source> 2. Become root in epyc 3. Go to /root/globus <source>cd /root/globus</source> 4. Insert and save the real paths at the end of this file (check commas for syntax or you'll get an error): <source>vim storage_gateway_path_restriction.js...")
• 19:45, 22 November 2023 Khtang talk contribs created page User talk:Bks.labmanager (Welcome!)
• 19:45, 22 November 2023 Khtang talk contribs created page User:Bks.labmanager (Creating user page for new user.)
• 19:45, 22 November 2023 User account Bks.labmanager talk contribs was created by Khtang talk contribs and password was sent by email
• 20:09, 27 October 2023 Frodo talk contribs created page ZINC22:Layers (asdf)
• 06:16, 21 September 2023 Iamkaant talk contribs created page Extended Search of Analogs via Bioisosteric Replacements (Created page with "=== Rationale === Our standard pipeline of searching for analogs (at least as I know it) consists of entering the SMILES of a molecule of interest into all flavors of SmallWorld and Arthor, available in the lab. This procedure has two drawbacks: # Limited diversity. SmallWorld's and Arthor's measure of distance between the analogs and the parent compound is graph edit distance.<ref>I am probably using slightly wrong terminology here, so be it. You can learn more about...")
• 21:42, 20 September 2023 Omailhot talk contribs created page Olivier's way of computing novelty (Created page with "This is my lazy way of doing novelty calculations. '''Step 0: source my environment''' All I'm developing is part of a single Python package called bksltk (BKS-lab Toolkit). So just source my Python environment on gimel2 (or other gimelX which has Python3) and you'll have access to everything: source /nfs/home/omailhot/pyenv_source.sh Eventually the package will be better documented (and probably integrated into pydock). '''Step 1: get all knowns from ChEMBL''' H...")
• 20:57, 20 September 2023 Khtang talk contribs created page Chemistry commons Notes (Created page with "== Database Management == Source chemistry commons source /nfs/soft/anaconda3/bin/activate ~khtang/.conda/envs/chemcommons === Import data from Spreadsheet === ** This will be deprecated once we switched to use postgres bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx] === Export Chemistry Commons DB === Run this script to create a snapshot of the database and JSON files for Enum...")
• 21:08, 12 September 2023 Jgutierrez6 talk contribs created page Rack Power (PDUs) (Created page with "== Introduction == This page will detail what PDUs are in which rack and how much Amperage they can hold. It will also detail how much max Amperage each machine can draw from the PDUs. == Power Table ==")
• 20:16, 29 August 2023 Ianscottknight talk contribs moved page TLDR:dude-z to TLDR:decoygen (Naming the decoy generation pipeline `dude-z` doesn't really make sense given that DUDE-Z is a dataset. I am guessing that the original logic behind this was that the pipeline was used to help create DUDE-Z. Still, the data types `pipeline` and `dataset` are distinct, therefore justifying this name change.)
• 01:44, 24 August 2023 Ianscottknight talk contribs created page File:Pydock3 logo.png
• 01:44, 24 August 2023 Ianscottknight talk contribs uploaded File:Pydock3 logo.png
• 18:51, 10 August 2023 Mtsukanov talk contribs created page CLI Enumeration (Created page with "== Coding the Reactions == Step 1. Pick out the reactions that you want to enumerate. This can be done either through already-made reactions that are in commons.docking.org or you can use those reaction SMARTS and inclusion/exclusion SMARTS as examples/guidelines to make your own reaction/s. We recommend using the daylight SMARTS as a resource if you plan on doing this: https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html. Once you have your reaction we recomme...")
• 00:13, 14 June 2023 Btingle talk contribs created page All About DB2 Files (Created page with "== The brass tacks == DB2 files encode & compress 3D molecule rotomers, sometimes referred to as conformations. DB2 files do not store the dihedral angles of rotomers, but instead the per-atom coordinates resulting from those angles Atoms of different rotomers whose coordinates overlap are merged together in db2 files (how this is done will be detailed more later), thus allowing DOCK to avoid double-calculating per-atom energies == The nitty gritty == DB2 is a text fo...")
• 22:21, 31 May 2023 Btingle talk contribs created page Installing The 3D Pipeline ZINC22 (Created page with "Installation of the 3D pipeline is somewhat tricky- the environment is very particular about which versions of which software should be used. It is thus easiest to copy the exact software packages we use from our servers- this should work provided they are installed in a 64-bit linux architecture, though depending on the distribution certain shared libraries may be missing. == Setting up the installation root == First find a suitable directory which will serve as the r...")
• 21:20, 23 May 2023 Mtsukanov talk contribs created page Particle Shape Calculator for CCDC/Mercury (Created page with "This tutorial will introduce you to the morphology calculation features included with Mercury under the CSD-Particle toolset, namely BFDH Morphology and VisualHabit. BFDH crystal morphology is an approximation based on crystallographic geometrical considerations. For a given structure, the BFDH algorithm will predict the habit or shape of a crystal using the corresponding unit cell and symmetry operator information. The VisualHabit tool calculates a morphology for your m...")
• 23:01, 1 May 2023 Iamkaant talk contribs created page File:Combined metrics plot from a GA run.png
• 23:01, 1 May 2023 Iamkaant talk contribs uploaded File:Combined metrics plot from a GA run.png
• 06:58, 30 April 2023 Iamkaant talk contribs created page Global Matching Sphere Optimization (Created page with "== Goal == To optimize your matching sphere (MS) setups getting more enrichment with fewer spheres. == Description == The program performs optimization of matching spheres using genetic algorithm. It selects spheres from two sets: * heavy atoms of xtal-lig * spheres prepared by SPHGEN program At each generation, N matching sphere sets are created, containing a maximum of M spheres each. Then retrospective docking is done for each set, and sets are ranked by the enrichme...")
• 21:57, 25 April 2023 Frodo talk contribs created page How to release DOCK (asdf)
• 19:02, 19 April 2023 Saadamin2006 talk contribs created page GPU DOCK (Created page with "# GPU DOCK Wiki GPU DOCK is a fork of DOCK 3.8 that utilizies GPU acceleration via CUDA. Currently (as of April 2023) GPU DOCK uses the GPU for parallel scoring and only supports Van der Waals, electrostatics, and solvation scores. # Running and Building GPU DOCK The main files for GPU DOCK are in the `DOCK/ucsfdock/docking/DOCK/src` directory of DOCK. There are a few important scripts here: * `clean.sh` that clears object files from previous builds * `compile.sh` wh...")
• 15:25, 19 April 2023 Frodo talk contribs created page User talk:Saadamin2006 (Welcome!)
• 15:25, 19 April 2023 Frodo talk contribs created page User:Saadamin2006 (Creating user page for new user.)
• 15:25, 19 April 2023 User account Saadamin2006 talk contribs was created by Frodo talk contribs and password was sent by email (welcome)
• 22:24, 12 April 2023 Frodo talk contribs created page Search (asdf)
• 17:40, 12 April 2023 Frodo talk contribs created page Standup tuesday (asdf)
• 18:16, 31 March 2023 Frodo talk contribs created page Properties (asdf)
• 16:10, 31 March 2023 Frodo talk contribs created page Installing DOCK6 on Apple Silicon M2 (asdf)
• 17:49, 23 March 2023 Frodo talk contribs created page OCI:More work (asdf)
• 19:49, 22 March 2023 Frodo talk contribs created page OCI:Create account (asdf)
• 18:35, 22 March 2023 Frodo talk contribs created page OCI:Set up account (asdf)
• 18:50, 21 March 2023 Mtsukanov talk contribs created page AB3 Developer Notes (Created page with "'''UNDER DEVELOPMENT''' The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a json file with all our reaction information as the first...")
• 22:24, 20 March 2023 Frodo talk contribs created page Covalent library preparation 2023 (qasdf)
• 20:21, 15 March 2023 Frodo talk contribs created page TLDR:enumeration (asdf)
• 19:42, 15 March 2023 Frodo talk contribs created page TLDR:bbfilter (asdf)
• 22:32, 13 March 2023 Khtang talk contribs created page LUNA (Created page with "'''LUNA''' is drug discovery Python toolkit developed by Keiser Lab at UCSF Github repo https://github.com/keiserlab/LUNA == Install Instruction == If you have trouble following LUNA's conda environment setup instruction, try this conda create -n luna-env -c schrodinger pymol -y conda activate luna-env conda install -c conda-forge rdkit seaborn openbabel pip xopen colorlog networkx -y pip install mmh3==2.5.1 pip install biopython==1.72 BKS Cluster has LUNA conda...")
• 20:29, 2 March 2023 Btingle talk contribs created page Repackaging DB2 DOCK38 (Created page with "The following is a script for repackaging 3D pipeline results. First, here is the script: <nowiki> #!/bin/bash # make_tarballs.bash # required parameter RESULT_DIRECTORY=$1 # optional parameters WORKING_DIRECTORY=${WORKING_DIRECTORY-/tmp/$(whoami)} PACKAGES_PER_PACKAGE=${PACKAGES_PER_PACKAGE-100} PACKAGE_TYPE=${PACKAGE_TYPE-db2.gz} PACKAGE_TYPE_SHORT=$(echo $PACKAGE_TYPE | cut -d'.' -f1) echo WORKING_DIRECTORY=$WORKING_DIRECTORY mkdir -p $WORKING_DIRECTORY && cd $WO...")
• 21:56, 22 February 2023 Jgutierrez6 talk contribs created page How to use Arthor Command Line (Created page with "== Introduction == Here is an introduction on how to use the Arthor commands in the command line for substructure searching. == Important Information == *Arthor Databases are backed up in '''/nfs/exj/arthor_db_backup/'''. *Arthor version will differ as time goes on but the command line should be fairly the same. == Simple use of Arthor Commands == # Export the Arthor bin path to use executables #: <source> export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-3.4.7/arthor...")
• 19:38, 21 February 2023 Jgutierrez6 talk contribs created page How to use Smallworld Java Command Line (Created page with "== How to use Smallworld Java Command Line == # Use bash as your shell #* <source>bash //just type in bash and enter</source> # Export these variables #* <source> export SWDIR=/mnt/nfs/db3/public_smallworld_5th_gen export sw='java -jar /nfs/db3/smallworld-5.5/sw.jar' </source> # Run the similarity command and it will display what it can do #* <source> $sw sim </source> # The path of the databases you can search from is here #* /mnt/nfs/db3/public_smallworld_5th_gen/maps/...")