Visualize docking grids - Revision history

Frodo: asdf

2024-05-25T00:26:01Z

asdf

← Older revision		Revision as of 00:26, 25 May 2024
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	Thanks Reed Stein and Trent Balius for writing those scripts.		Thanks Reed Stein and Trent Balius for writing those scripts.


			[[Category:Grids]]
			[[Category:Visualization]]

Jklyu at 23:11, 9 March 2018

2018-03-09T23:11:31Z

← Older revision		Revision as of 23:11, 9 March 2018
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	2.4) select .dx files you want to visualize		2.4) select .dx files you want to visualize


	Thanks Reed Stein and Trent Balius for writing those scripts.		Thanks Reed Stein and Trent Balius for writing those scripts.

Jklyu at 23:10, 9 March 2018

2018-03-09T23:10:29Z

← Older revision		Revision as of 23:10, 9 March 2018
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	The output should be ligdesolv.dx		The output should be ligdesolv.dx



	2) Visualize grids in Chimera		2) Visualize grids in Chimera
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	2.4) select .dx files you want to visualize		2.4) select .dx files you want to visualize

			Thanks Reed Stein and Trent Balius for writing those scripts.

Jklyu at 23:09, 9 March 2018

2018-03-09T23:09:08Z

← Older revision		Revision as of 23:09, 9 March 2018
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	The output should be vdw_energies_repulsive.dx, vdw_energies_attractive.dx and vdw.dx.		The output should be vdw_energies_repulsive.dx, vdw_energies_attractive.dx and vdw.dx.

	1.2) The ~~electrostatic~~ grid		1.2) The electrostatics grid

	python /mnt/nfs/home/jklyu/zzz.script/pymol_movie/phi_to_dx.py trim.electrostatics.phi trim.electrostatics.dx		python /mnt/nfs/home/jklyu/zzz.script/pymol_movie/phi_to_dx.py trim.electrostatics.phi trim.electrostatics.dx
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	1.3) The desolvation grid		1.3) The desolvation grid

			python /mnt/nfs/home/jklyu/zzz.script/pymol_movie/create_LigDeSolv_DX.py

			The output should be ligdesolv.dx

	2) Visualize grids in Chimera		2) Visualize grids in Chimera

			2.1) Open the Chimera

			2.2) Go to Tools --> Volume Data --> Volume Viewer

			2.3) File --> Open map

			2.4) select .dx files you want to visualize

Jklyu at 23:04, 9 March 2018

2018-03-09T23:04:11Z

← Older revision		Revision as of 23:04, 9 March 2018
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	1) Convert grids into a format that Chimera can read in		1) Convert grids into a format that Chimera can read in

	1.1) The vdw ~~grid~~		cd /your/dock/path/dockfiles

			1.1) The VDW grid

			python /mnt/nfs/home/jklyu/zzz.script/pymol_movie/create_VDW_DX.py

			The output should be vdw_energies_repulsive.dx, vdw_energies_attractive.dx and vdw.dx.

	1.2) The electrostatic grid		1.2) The electrostatic grid

			python /mnt/nfs/home/jklyu/zzz.script/pymol_movie/phi_to_dx.py trim.electrostatics.phi trim.electrostatics.dx

			The output should be trim.electrostatics.dx.

	1.3) The desolvation grid		1.3) The desolvation grid



	2) Visualize grids in Chimera		2) Visualize grids in Chimera

Jklyu: Created page with "Written by Jiankun Lyu, 20180309 1) Convert grids into a format that Chimera can read in 1.1) The vdw grid 1.2) The electrostatic grid 1.3) The desolvation grid 2) Visual..."

2018-03-09T22:57:16Z

Created page with "Written by Jiankun Lyu, 20180309 1) Convert grids into a format that Chimera can read in 1.1) The vdw grid 1.2) The electrostatic grid 1.3) The desolvation grid 2) Visual..."

New page

Written by Jiankun Lyu, 20180309

1) Convert grids into a format that Chimera can read in

1.1) The vdw grid

1.2) The electrostatic grid

1.3) The desolvation grid

2) Visualize grids in Chimera