Reply To: ddg Script Problem

[Anonymous]

Sure, sorry…

http://www.pyrosetta.org/scripts

Here’s a snippet:

dock_jump = 1
interface_dist = 8.0 #angstroms
DockingProtocol().setup_foldtree(p)

scorefxn = create_score_function(‘standard’)
scorefxn(p) #needed for proper Interface calculation

interface = Interface(dock_jump)
interface.distance(8.0)

interface.calculate(p)
starting_p.assign(p)

ddg_scorefxn = ScoreFunction()
ddg_scorefxn.set_weight(fa_atr, 0.44)
ddg_scorefxn.set_weight(fa_rep, 0.07)
ddg_scorefxn.set_weight(fa_sol, 1.0)
ddg_scorefxn.set_weight(hbond_bb_sc, 0.5)
ddg_scorefxn.set_weight(hbond_sc, 1.0)

for i in range(1, p.total_residue()+1):
if (interface.is_interface(i) == True):
p.assign(starting_p)
ddg = interface_ddg(p, i, ‘A’)
f = open(“ala_scan_output.txt”, ‘a’)
mutname = p.pdb_info().chain(i)+str(p.pdb_info().number(i))+p.sequence()[i-1]+”to”+’A’+”.pdb”
f.write( mutname + ” ddG: ” + str(round(ddg, 3)) +’n’)

Thanks.