Datasets:
| from pymol import cmd,stored | |
| set depth_cue, 1 | |
| set fog_start, 0.4 | |
| set_color b_col, [36,36,85] | |
| set_color t_col, [10,10,10] | |
| set bg_rgb_bottom, b_col | |
| set bg_rgb_top, t_col | |
| set bg_gradient | |
| set spec_power = 200 | |
| set spec_refl = 0 | |
| load "data/umod.pdb", protein | |
| create ligands, protein and organic | |
| select xlig, protein and organic | |
| delete xlig | |
| hide everything, all | |
| color white, elem c | |
| color bluewhite, protein | |
| #show_as cartoon, protein | |
| show surface, protein | |
| #set transparency, 0.15 | |
| show sticks, ligands | |
| set stick_color, magenta | |
| # SAS points | |
| load "data/umod.pdb_points.pdb.gz", points | |
| hide nonbonded, points | |
| show nb_spheres, points | |
| set sphere_scale, 0.2, points | |
| cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7) | |
| stored.list=[] | |
| cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP | |
| lastSTP=stored.list[-1] # get the index of the last residue | |
| hide lines, resn STP | |
| cmd.select("rest", "resn STP and resi 0") | |
| for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index)) | |
| for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index)) | |
| for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index)) | |
| for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index)) | |
| set_color pcol1 = [0.361,0.576,0.902] | |
| select surf_pocket1, protein and id [1737,1740,2309,1742,1953,1959,1994,1997,1728,1732,1734,2283,2307,2263,2265,2275,2276,2278,2282] | |
| set surface_color, pcol1, surf_pocket1 | |
| deselect | |
| orient | |