The script below demonstrates how to use the cluster_cut argument to transfer_xyz to make a clustered representative of a set of PDB files of the same sequence.
1 from modeller import *
2
3 def cluster_pdbs(e, pdbs, cluster_cut):
4 """Get a representative of a set of PDBs.
5 Every PDB file must be a structure of the same sequence.
6 The representative model is returned."""
7 a = alignment(e)
8
9 # Read all structures, and make a 1:1 alignment of their sequences
10 for filename in pdbs:
11 m = model(e, file=filename)
12 a.append_model(m, align_codes=filename, atom_files=filename)
13
14 # Structurally superimpose all structures without changing the alignment
15 a.malign3d(gap_penalties_3d=(0, 3), fit=False)
16
17 # Add a new dummy model with the same sequence to hold the cluster
18 m = model(e, file=pdbs[0])
19 a.append_model(m, align_codes='cluster', atom_files='cluster')
20
21 # Make the clustered representative
22 m.transfer_xyz(a, cluster_cut=cluster_cut)
23 return m
24
25
26 # Filenames to cluster
27 pdbs = ("1fdx.B99990001.pdb", "1fdx.B99990002.pdb", "1fdx.B99990003.pdb")
28
29 e = environ()
30 m = cluster_pdbs(e, pdbs, 1.5)
31 m.write(file='cluster.pdb')
