Tutorial on running DOCK3.7 with blury-GIST: Difference between revisions
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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: | ||
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. | |||
* 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 | |||
Latest revision as of 19:39, 17 November 2017
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:
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.
- 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