Hi, All, I am writing a script to find all salt bridges in a pentameric proteins in 50 models.
The issues are 1. There are no salt bridges found in the same chain. But I find some if I use this command. >pairwise_dist /model00000//A/LYS+ARG/NZ+NE+NH*, >/model00000//A/ASP+GLU/OD*+OE*, 4, show=N, output=P My guess is that pairwise_dist does not take the same sel1, sel2 as a valid input. Any solutions/suggestions? 2. The script is apparently not optimized. Any suggestions? Thanks! Charles Here are what I am using now. from pymol import cmd from glob import glob for file in glob("model*.pdb"): print(file) cmd.load(file) obj=cmd.get_object_list('all') print(obj) #salt bridge cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_A") cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_B") cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_C") cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_D") cmd.do("pairwise_dist ///A/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_A_E") cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_B") cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_C") cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_D") cmd.do("pairwise_dist ///B/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_B_E") cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_C") cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_D") cmd.do("pairwise_dist ///C/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_C_E") cmd.do("pairwise_dist ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_D_D") cmd.do("pairwise_dist ///D/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_D_E") cmd.do("pairwise_dist ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, ///E/ASP+GLU+LYS+ARG/OD*+OE*+NZ+NE+NH*, 4, show=N, output="+str(obj[0])+"_E_E") cmd.delete("all")
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