Difference between revisions of "Matching Sphere Scan"

From DISI
Jump to: navigation, search
Line 13: Line 13:
 
Trent's original script is located here:
 
Trent's original script is located here:
  
    python ~tbalius/zzz.scripts/make_random_sph_non_ligand.py {INPUT_SPHERE_FILE} {maximum distance to perturb spheres} {OUTPUT_SPHERE_NAME}
+
    python ~tbalius/zzz.scripts/make_random_sph_non_ligand.py {INPUT_SPHERE_FILE} {maximum distance to perturb spheres} {OUTPUT_SPHERE_NAME}
  
  
 
Note that the "random spheres" in the original matching_spheres.sph file have a "0.000" in the fifth column. This is changed to 0.5 after perturbing the matching spheres. If you would like to perturb the matching spheres again after you have already run it, the fifth column with "0.500" needs to be changed back to "0.000"
 
Note that the "random spheres" in the original matching_spheres.sph file have a "0.000" in the fifth column. This is changed to 0.5 after perturbing the matching spheres. If you would like to perturb the matching spheres again after you have already run it, the fifth column with "0.500" needs to be changed back to "0.000"

Revision as of 10:57, 15 May 2020

This script generates some number of directories with perturbed matching spheres. This will randomly perturb non-crystallographic spheres generated by SPHGEN during blastermaster.

The original script was written by Trent Balius. Wrapper script is written by Reed Stein.

Usage:

   python ~rstein/zzz.scripts/sphere_sets_scripts/generate_non_xtal_spheres_dirs.py {YOUR_DOCK_DIR} {# directories to generate} {maximum distance to perturb spheres}

So if you wanted to generate 100 new docking directories with 100 different perturbed matching sphere setups (randomly differing from the original matching spheres by at maximum 0.5 Å), use the command:

   python ~rstein/zzz.scripts/sphere_sets_scripts/generate_non_xtal_spheres_dirs.py DOCK_DIR/ 100 0.5

Trent's original script is located here:

   python ~tbalius/zzz.scripts/make_random_sph_non_ligand.py {INPUT_SPHERE_FILE} {maximum distance to perturb spheres} {OUTPUT_SPHERE_NAME}


Note that the "random spheres" in the original matching_spheres.sph file have a "0.000" in the fifth column. This is changed to 0.5 after perturbing the matching spheres. If you would like to perturb the matching spheres again after you have already run it, the fifth column with "0.500" needs to be changed back to "0.000"