ZINC22:Building 3D - Revision history

Btingle: Redirected page to Building The 3D Pipeline ZINC22

2023-03-09T18:07:53Z

Redirected page to Building The 3D Pipeline ZINC22

← Older revision		Revision as of 18:07, 9 March 2023
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			#REDIRECT [[Building The 3D Pipeline ZINC22]]

	This describes how to become a contributor to ZINC-22		This describes how to become a contributor to ZINC-22

Frodo: asdf

2021-01-29T01:14:14Z

asdf

← Older revision		Revision as of 01:14, 29 January 2021
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			This describes how to become a contributor to ZINC-22

			= Step 1. Download DOCK.3.8 and other software =
	= 1. Download DOCK.3.8 =
	* Note: DOCK.3.8 has a lot of software in it, which can make it a bit expensive to throw in a software image.		* 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.		* 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		* 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.
	* also at files.docking.org/private/software/DOCK.3.8.0.3d.tar.gz. chemistry4biology at gmail dot com for credentials		Ask chemistry4biology at gmail dot com for credentials

	* Download python3 environment (lig_build_py3-3.7.1.tar.gz)		* Download python3 environment (lig_build_py3-3.7.1.tar.gz)
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	* Clone submission scripts to somewhere you can use them. (https://github.com/btingle/zinc-3d-build-3.git)		* 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 ~~and at files~~.~~docking~~.~~org/private/software/~~		* All tar.gz can be found in /nfs/home/xyz/soft on our cluster. Ask JJI about remote access.

	= 2. Setup for running 3d building =		= Step 2. Setup for running 3d building =

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

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

	* [[ZINC22:Checkout]]		* [[ZINC22:Checkout]]

	~~[[Category:ZINC22]]~~

	= 4. Run 3D building (at scale) =		= 4. Run 3D building (at scale) =
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	= 6. Lather, rinse, repeat, go back to step 3 =		= 6. Lather, rinse, repeat, go back to step 3 =


	[[Category:ZINC22]]		[[Category:ZINC22]]

Frodo: /* 5. Check 3D back into UCSF Central server */

2021-01-28T01:12:26Z

5. Check 3D back into UCSF Central server

← Older revision		Revision as of 01:12, 28 January 2021
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	= 5. Check 3D back into UCSF Central server =		= 5. Check 3D back into UCSF Central server =

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

Frodo: /* 6. Later rise repeat, go back to step 3 */

2021-01-28T01:11:56Z

6. Later rise repeat, go back to step 3

← Older revision		Revision as of 01:11, 28 January 2021
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	* [[ZINC22:Checkin 3D]]		* [[ZINC22:Checkin 3D]]

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


	[[Category:ZINC22]]		[[Category:ZINC22]]

Frodo: /* 1. Download DOCK.3.8 */

2021-01-28T01:10:25Z

1. Download DOCK.3.8

← Older revision		Revision as of 01:10, 28 January 2021
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	* 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.		* 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		* You can find this version at /nfs/home/xyz/soft/DOCK.3.8.0.3d.tar.gz
	* also at files.docking.org/private/DOCK.3.8.0.3d.tar.gz. chemistry4biology at gmail dot com for credentials		* also at files.docking.org/private/software/DOCK.3.8.0.3d.tar.gz. chemistry4biology at gmail dot com for credentials

	* Download python3 environment (lig_build_py3-3.7.1.tar.gz)		* Download python3 environment (lig_build_py3-3.7.1.tar.gz)
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	* All tar.gz can be found in /nfs/home/xyz/soft on our cluster and at files.docking.org/private/software/		* All tar.gz can be found in /nfs/home/xyz/soft on our cluster and at files.docking.org/private/software/


	= 2. Setup for running 3d building =		= 2. Setup for running 3d building =

Frodo: /* 5. Check 3D back into UCSF Central server */

2021-01-27T19:16:54Z

5. Check 3D back into UCSF Central server

← Older revision		Revision as of 19:16, 27 January 2021
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	= 5. Check 3D back into UCSF Central server =		= 5. Check 3D back into UCSF Central server =

	* need credentials		* you need credentials
			* [[ZINC22:Checkin 3D]]

	= 6. Later rise repeat, go back to step 3 =		= 6. Later rise repeat, go back to step 3 =

Frodo: /* 3. Check out SMILES from the central server for building */

2021-01-27T19:16:02Z

3. Check out SMILES from the central server for building

← Older revision		Revision as of 19:16, 27 January 2021
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	* Copy your jchem license to ~/.jchem-license.cxl		* Copy your jchem license to ~/.jchem-license.cxl

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

			* [[ZINC22:Checkout]]

			[[Category:ZINC22]]

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

Frodo: asdf

2021-01-27T19:14:59Z

asdf

New page

= 1. Download DOCK.3.8 =
* 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
* also at files.docking.org/private/DOCK.3.8.0.3d.tar.gz. 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 and at files.docking.org/private/software/

= 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

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

= 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 =

* need credentials

= 6. Later rise repeat, go back to step 3 =

[[Category:ZINC22]]