Difference between revisions of "Tutorial on running DOCK3.7 with blury-GIST"

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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.

Latest revision as of 12:39, 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