In case anyone has a similar problem, here is my solution
from pymol import cmd
from glob import glob
cmd.do("run list_hb.py")
for file in glob("model*.pdb"):
print(file)
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#hydrogen bonds
cmd.do("list_hb all, all, write_distances_file=hb_"+str(obj[0])+".txt")
#salt bridge
cmd.do("select negative, (resn ASP+GLU and name OD*+OE*)")
cmd.do("select positive, (resn Lys and name NZ) or (resn ARG and name NE +
NH*)")
cmd.do("pairwise_dist negative, positive, 4, show=N, output="+str(obj[0]))
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Today's Topics:
1. Salt bridges in same chains (Chen, Qiang)
----------------------------------------------------------------------
Message: 1
Date: Wed, 10 Feb 2021 15:09:28 +0000
From: "Chen, Qiang" <q...@pitt.edu>
To: "pymol-users@lists.sourceforge.net"
<pymol-users@lists.sourceforge.net>
Subject: [PyMOL] Salt bridges in same chains
Message-ID:
<dm6pr04mb4667a3774965c75ab387beb9fa...@dm6pr04mb4667.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
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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