Hi, everyone:
I want to generate pos file for different scaffolds, and I find that gen_apo_grid can satisfy my needs. But there is a problem, if this option "-packstat:surface_accessibility" is on, I can set the value of "-packstat:min_surface_accessibility". Whatever value I set for "-packstat:min_surface_accessibility", the output pos file does not change at all.
Example Command Lines:
-s a.pdb
-chname off
-constant_seed
-ignore_unrecognized_res
-packstat:surface_accessibility true
-packstat:cavity_burial_probe_radius 2.0
-packstat:cluster_min_volume 150
-packstat:min_cluster_overlap 0.1
-packstat:min_cav_ball_radius 1.5
-packstat:min_surface_accessibility 999999999
-s a.pdb
-chname off
-constant_seed
-ignore_unrecognized_res
-packstat:surface_accessibility true
-packstat:cavity_burial_probe_radius 2.0
-packstat:cluster_min_volume 150
-packstat:min_cluster_overlap 0.1
-packstat:min_cav_ball_radius 1.5
-packstat:min_surface_accessibility 0.5
These two commands gives me the same output, that's really strange! And if I turn off the "-packstat:surface_accessibility", the program won't do "prune" option every 0.1 radius anymore. I went to see the original C++ code, and I find that there are some codes:
//if swicth is on, do more calculation
if ( surface_accessibility ) {
for ( PackstatReal pr = burial_radius-0.1; pr >= 0.1; pr -= 0.1 ) {
opts.prune_cavity_burial_probe_radii.push_back(pr);
}
}
This is the cause for "prune" option every 0.1 radius. But it seems that this operation has nothing to do with that "-packstat:min_surface_accessibility".
Please anyone can help me to understand how to make this work?
Thanks very much for your time and effort!
JaosnIsaac