View source for ZINC22:Building 3D

#REDIRECT [[Building The 3D Pipeline ZINC22]]

This describes how to become a contributor to ZINC-22

= Step 1. Download DOCK.3.8 and other software =
* Note: DOCK.3.8 has a lot of software in it, which can make it a bit expensive to throw in a software image.
* When 3D building, only a small portion of the DOCK software is used, so at the lab we have a "stripped down" version of DOCK for 3d building.
* You can find this version at /nfs/home/xyz/soft/DOCK.3.8.0.3d.tar.gz and also at files.docking.org/private/software/DOCK.3.8.0.3d.tar.gz.
Ask chemistry4biology at gmail dot com for credentials

* Download python3 environment (lig_build_py3-3.7.1.tar.gz)
* Download Jchem 19.15 (jchem-19.15.tar.gz)
* Download Corina (supply your own corina executable, name the folder it resides in corina, tar that folder up into corina.tar.gz)
* Download Libraries (lib.tar.gz)
* Clone submission scripts to somewhere you can use them. (https://github.com/btingle/zinc-3d-build-3.git)

* All tar.gz can be found in /nfs/home/xyz/soft on our cluster. Ask JJI about remote access. 

= Step 2. Setup for running 3d building =

* Move the software you downloaded to a folder named ~/soft.
* Copy your openeye license to ~/.oe-license.txt
* Copy your jchem license to ~/.jchem-license.cxl

= Step 3. Check out SMILES from the central server for building =

* [[ZINC22:Checkout]]

= 4. Run 3D building (at scale) = 

* [[Building_The_3D_Pipeline_ZINC22]] for information on running the script.

= 5. Check 3D back into UCSF Central server = 

* you need credentials ask chemistry4biology at gmail dot com
* [[ZINC22:Checkin 3D]]

= 6. Lather, rinse, repeat, go back to step 3 = 

[[Category:ZINC22]]