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  • ZINC22:Building 3D
    * Download Jchem 19.15 (jchem-19.15.tar.gz) * Copy your jchem license to ~/.jchem-license.cxl
    2 KB (269 words) - 18:07, 9 March 2023
  • Web Tools
    * [http://www.chemaxon.com/instantjchem/ Instant JChem]
    741 bytes (97 words) - 04:38, 14 February 2014
  • Nailgun
    ...fan/NAILGUN/nailgun-master/nailgun-examples/target/classes:/nfs/soft/jchem/jchem-19.15/lib/*" As for Jchem, I don't know why it works, but it does :)
    2 KB (300 words) - 20:52, 18 March 2020
  • Converting SMILES to Kekule Format
    /nfs/soft/jchem/current/bin/molconvert smiles:-a {INPUT_SMILES.smi} > {OUTPUT_SMILES.smi}
    558 bytes (88 words) - 19:39, 30 October 2019
  • Installing The 3D Pipeline ZINC22
    ...axon licenses to the licenses directory- name them ".oe-license.txt" and ".jchem-license.cxl", respectively. .jchem-license.cxl
    2 KB (368 words) - 22:21, 31 May 2023
  • Installing oracle
    '''Installation of Oracle and JChem Cartridge''' Abbreviated instructions on how Oracle Enterprise 11g and ChemAxon's JChem Cartridge was installed on erindev.bkslab.org
    5 KB (754 words) - 18:33, 12 March 2014
  • Testing zinc21
    * jchem version
    785 bytes (106 words) - 22:35, 1 July 2019
  • Ligand preparation - 20170424
    == set up environment: jchem mitools, DOCK3.7, ZINC, corina == source /nfs/soft/jchem/current/env.csh
    5 KB (726 words) - 22:53, 17 November 2017
  • Pka
    ...mics can apply for a free academic license. Lab copy is in /raid3/software/jchem/current/bin/mview. You have to cd to that directory then run it.
    1 KB (255 words) - 10:48, 5 June 2014
  • Oracle scraps
    ...erations, tdf:y option has to be set for the jchem index or the underlying JChem table.
    5 KB (681 words) - 17:01, 18 March 2014
  • DUD
    |Dependencies = [[JChem]], [[ChemAxon]]
    2 KB (284 words) - 20:44, 3 January 2019
  • Cassidy clustering
    /raid3/software/jchem/current/bin/generatemd c emol_p0.smi -k CF -f 1024 -2 | /raid1/people/teagu
    2 KB (288 words) - 07:22, 13 March 2014
  • ZINC22:Singularity
    export CHEMAXON_LICENSE_URL=$LICENSE_DIR/jchem-license.cxl
    2 KB (355 words) - 21:40, 9 February 2021
  • Building The 3D Pipeline ZINC22
    ...our licensed software includes jchem and openeye, licenses must be named .jchem-license.cxl and .oe-license.txt respectively. if you're sourcing a premade jchem-latest -> jchem-19.15_r1.tar.gz
    10 KB (1,616 words) - 18:11, 9 March 2023
  • Methods section
    ...om ZINC (http://zinc15.docking.org), and protonation states and tautomers (Jchem v15.11.23.0, www.chemaxon.com), 3D structures (Corina v3.6.0026, www.molecu ...0, and low, roughly pH 5.8 to 6.4. Each protomer is rendered into 3D using Jchem’s molconvert (ChemAxon, Budapest, Hungary) and conformationally sampled u
    2 KB (328 words) - 21:37, 7 April 2022
  • Install DOCK 3.7
    ...for building your own databases. If you use ZINC, you do not need OpenEye, Jchem, Corina or AMSOL.)
    3 KB (486 words) - 20:53, 19 April 2024
  • ZINC15:current limitations
    ITP - axial equatorial of corina vs jchem molconvert.
    3 KB (550 words) - 14:52, 10 October 2015
  • Generating decoys (Reed's way)
    Additionally, JChem needs to be sourced in your ~/.cshrc file with the command: source /nfs/soft/jchem/current/env.csh
    14 KB (2,220 words) - 07:49, 23 September 2022
  • How to use Arthor API
    ..., in future there may be new URLs introduced to match other clients (e.g. /jchem/).
    6 KB (901 words) - 20:50, 16 February 2023
  • DUDE
    |Dependencies = [[JChem]], [[ChemAxon]]
    12 KB (1,955 words) - 20:35, 4 January 2019
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