from pymol import cmd, stored, math
import time
-cmd.load('plik.pdb')
-mol='plik'
+with open('plik.pdb') as f, open('plik1.pdb', 'w') as f1:
+ prev_ires=None
+ ires = 0
+ for line in f:
+ if line[0:6] == 'ATOM ':
+ if line[22:26] != prev_ires:
+ prev_ires=line[22:26]
+ ires += 1
+ f1.write(line[:22]+str(ires).rjust(4)+line[26:])
+ elif line[0:3] == 'TER':
+ f1.write(line)
+
+cmd.load('plik1.pdb')
+mol='plik1'
obj=cmd.get_object_list(mol)[0]
inFile = open('fluctuations.txt', 'r')
cmd.show_as("cartoon",mol)
cmd.cartoon("putty", mol)
+cmd.show("sticks","(cys/ca+cb+sg) and byres (cys/sg and bound_to cys/sg)")
cmd.set("cartoon_putty_scale_min", min(bfacts),obj)
cmd.set("cartoon_putty_scale_max", max(bfacts),obj)
cmd.set("cartoon_putty_transform", 7,obj)