Datasets:
File size: 2,257 Bytes
3c49a60 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 |
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/f10a.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/f10a.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 [2781,2785,3042,3045,3563,3018,3167,3171,3028,3015,3031,3026,3032,2782]
set surface_color, pcol1, surf_pocket1
set_color pcol2 = [0.702,0.278,0.533]
select surf_pocket2, protein and id [2760,2762,2769,2723,2729,2730,1023,1106,2732,2735,1024,1027,1031]
set surface_color, pcol2, surf_pocket2
deselect
orient
|