Tutorial on running DOCK3.7 with blury-GIST - Revision history

TBalius at 19:39, 17 November 2017

2017-11-17T19:39:48Z

← Older revision		Revision as of 19:39, 17 November 2017
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	Use the following command to truncated the GIST grids:		Use the following command to truncated the GIST grids:

	python /path/GIST_DX_tools/src/dx-remove_extrema.py input.dx value ouput_prifix > truncate.log		python /path/GIST_DX_tools/src/dx-remove_extrema.py input.dx value ouput_prifix > truncate.log

	if value = 3.0 kcal/mol/anstroms^3 then the max any on voxel can contribute is 0.375 kcal/mol.		if value = 3.0 kcal/mol/anstroms^3 then the max any on voxel can contribute is 0.375 kcal/mol.
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	Use the following python script to blur GIST grids:		Use the following python script to blur GIST grids:

	/path/GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix		python /path/GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix

	Note that the blurring process will shrink the grids slightly by the sphere radius.		Note that the blurring process will shrink the grids slightly by the sphere radius.

TBalius at 19:38, 17 November 2017

2017-11-17T19:38:37Z

← Older revision		Revision as of 19:38, 17 November 2017
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			first we truncate the grids. That is we cap the max magnitude any on voxel can contribute to the score.
			Use the following command to truncated the GIST grids:

			python /path/GIST_DX_tools/src/dx-remove_extrema.py input.dx value ouput_prifix > truncate.log

			if value = 3.0 kcal/mol/anstroms^3 then the max any on voxel can contribute is 0.375 kcal/mol.

	Use the following python script to blur GIST grids:		Use the following python script to blur GIST grids:

	GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix		/path/GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix

	Note that the blurring process will shrink the grids slightly by the sphere radius.		Note that the blurring process will shrink the grids slightly by the sphere radius.

			* set divider to 2.0

			We will generate two grids one for heavy atoms and one for hydrogens:
			* radius = 1.8, pad_radius = 1.8
			* radius = 1.0, pad_radius = 1.8

TBalius at 16:43, 16 November 2017

2017-11-16T16:43:23Z

← Older revision		Revision as of 16:43, 16 November 2017
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	GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix		GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix

	Note the ~~the burring~~ process will shrink the grids slightly by the sphere radius.		Note that the blurring process will shrink the grids slightly by the sphere radius.

TBalius: Created page with " Use the following python script to blur GIST grids: GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix Note the ..."

2017-11-15T20:09:23Z

Created page with " Use the following python script to blur GIST grids: GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix Note the ..."

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Use the following python script to blur GIST grids:

GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix

Note the the burring process will shrink the grids slightly by the sphere radius.