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  • Build new dock64 docker image
    * docker build -t jji/dockaws:latest * sudo docker push btingle/dockaws:latest (btingle or jji)
    231 bytes (41 words) - 17:23, 13 April 2021
  • DOCK Blaster:Suggestions
    -- jji . Feb 9 2008 [[Category:jji]]
    485 bytes (72 words) - 06:35, 14 February 2014
  • OCI:install client locally
    Tennancy jji user jji@cgl.ucsf.edu
    864 bytes (140 words) - 23:39, 23 February 2022
  • ZINC maintenance
    [[Category:jji]]
    102 bytes (16 words) - 05:27, 14 February 2014
  • Control of bkslab.org
    contact jji for more info.
    105 bytes (16 words) - 20:56, 2 February 2021
  • Web Tools
    * [http://www.collaborativedrug.com/ Collaborative Drug . com ] - ask jji for your password
    741 bytes (97 words) - 04:38, 14 February 2014
  • Similar products
    [[Category:jji]]
    203 bytes (33 words) - 04:24, 14 February 2014
  • Requests for ZINC
    [[Category:jji]]
    303 bytes (39 words) - 04:14, 14 February 2014
  • Drugs sans targets
    [[Category:jji]]
    808 bytes (108 words) - 20:35, 14 February 2014
  • Create an aws ec2 image
    * ssh -i /mnt/nfs/home/jji/.aws/terminal/newpair.pem ubuntu@ec2-18-216-90-202.us-east-2.compute.amazon
    388 bytes (63 words) - 05:53, 19 April 2021
  • John's Tips
    [[Category:jji]]
    423 bytes (70 words) - 20:34, 14 February 2014
  • ZINC scripts
    # jji. July 2012 - read list of ZINC ids from stdin, output mol2 files, referenc
    361 bytes (57 words) - 13:38, 1 May 2014
  • Workflow
    [[Category:jji]]
    838 bytes (118 words) - 06:05, 13 March 2014
  • Screen
    raiders 54 (jji, Feb 5, 2014)
    352 bytes (48 words) - 19:03, 28 June 2016
  • New 3D Building On Wynton
    the script is based in ~/zinc-3d-build-3 on jji@wynton Each job saves its results tarball to /wynton/scratch/jji/$SRC_FILENAME/$BATCH_ID/$END_ID.tar.gz
    2 KB (404 words) - 22:46, 16 July 2020
  • Unpack-repack
    ~jji/bin/sync.csh
    602 bytes (95 words) - 21:29, 29 July 2021
  • Protein-Protein Docking
    maksph - jji code to make focusing spheres from main spheres for protein work
    916 bytes (154 words) - 17:41, 15 February 2014
  • Zinc15 decoys
    *** in progress by jji ***
    693 bytes (121 words) - 00:34, 24 December 2015
  • Tunnel how to
    [Category:jji]]
    729 bytes (109 words) - 20:36, 31 August 2022
  • ZINC minisubsets
    [[Category:jji]]
    788 bytes (129 words) - 05:30, 14 February 2014
  • Cluster 3
    ...led under user jji on the QB3 cluster. You can copy .cshrc (.bashrc) from jji to get started.
    2 KB (407 words) - 06:25, 3 June 2015
  • Globus Curator's Guide
    "/nfs/exe/work/jji/2dexport", "/nfs/exe/work/jji/3d-zinc20",
    3 KB (425 words) - 21:06, 20 March 2024
  • Zinc22 restart wynton
    * copy from /wynton/group/bks/work/jji/p1/super
    985 bytes (161 words) - 05:46, 19 January 2021
  • Cluster 0 account
    ....login and .cshrc from ~jji/ ; If you use bash, copy .bash_profile from ~jji/
    3 KB (446 words) - 14:47, 23 April 2014
  • One time funky gene name cleanup
    era - summer 2016. jji
    1 KB (250 words) - 21:02, 8 September 2016
  • Qconf-mrqs
    limit users {jji,xyz,www,supritha} to slots=1300
    2 KB (239 words) - 23:43, 15 June 2018
  • Cluster 0
    hiers - Centos 5.3 - Server for jji jji
    6 KB (769 words) - 00:10, 9 April 2017
  • LoadingZINC21
    source ~jji/cshrc.save
    2 KB (304 words) - 19:10, 22 March 2024
  • ZINC22:Building 3D
    * All tar.gz can be found in /nfs/home/xyz/soft on our cluster. Ask JJI about remote access.
    2 KB (269 words) - 18:07, 9 March 2023
  • Customize shell
    #setenv DOCK_BASE /raid1/people/jji/dockenv
    2 KB (355 words) - 00:24, 23 October 2012
  • Zinc15 curators notes
    as jji. based on exported smiles,sub_id from zinc8 since last update.
    2 KB (320 words) - 18:40, 6 September 2016
  • Ipynb idioms
    path = '/nfs/home/jji/ipynb/data/test.smi'
    2 KB (312 words) - 23:30, 1 October 2015
  • ZINC processing pipeline
    [[Category:jji]]
    2 KB (348 words) - 05:28, 14 February 2014
  • WINC annotations
    [[Category:jji]]
    3 KB (487 words) - 04:37, 14 February 2014
  • Tool-selector
    * please comment directly to JJI (bugs, feature requests, poor choices, suggestions, etc)
    3 KB (461 words) - 19:46, 3 November 2016
  • XML RPC Procedures
    [[Category:jji]]
    3 KB (484 words) - 05:22, 14 February 2014
  • Analyzing DOCK 3.7 Results
    ...ogle.com/site/dock37wiki/home/analyzing-dock3-7-results on Feb 13, 2014 by jji.
    3 KB (601 words) - 21:22, 13 February 2014
  • DOCK Blaster:FAQ
    ...is supported by the US National Institutes of Health via grant GM71896 (to JJI and BKS). We reserve the right to limit usage by intensive users. You may request a copy of DOCK Blaster by writing to John Irwin at jji at cgl dot ucsf dot edu. We will be making the scripts available, but it w
    9 KB (1,448 words) - 22:06, 5 April 2013
  • Install DOCK 3
    jji@docking.org
    4 KB (573 words) - 06:41, 13 March 2014
  • DOCK 3.7
    * [[Running docking 3.7]] - JJI currently working on this.
    6 KB (844 words) - 17:03, 27 July 2021
  • Build ChEMBL for SEA
    cd ~khtang/jji/
    6 KB (922 words) - 21:19, 22 June 2023
  • TLDR
    ...s: Works with special cases only. Nearly ready to use. If interested, ask jji for assistance.
    6 KB (941 words) - 20:27, 29 April 2024
  • Slurm
    sudo sacctmgr add user jji account=bks
    11 KB (1,517 words) - 23:06, 7 February 2023
  • How to dock in DOCK3.8
    export DOCKBASE=/wynton/group/bks/work/jji/DOCK
    16 KB (2,599 words) - 22:28, 1 December 2022
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