[MMTK] about reading pdb files

Peter peter at maubp.freeserve.co.uk
Thu Jun 10 11:35:21 CEST 2004


Hua Wong,
 
Its probably easier to open the whole PDB file in MMTK, and then select the residues you want (rather than editing the PDB file first).
 
Here is an example using the first chain of insulin.

(Note I have not tried to do anything with this sub chain except visualise it)
 
Peter
 
----------------------------------------------------------------
 
from MMTK import *
from MMTK.Proteins import Protein

print "Loading protein file"
#Insulin has four chains, only going to look at the first one
full_chain = Protein('insulin')[0]

sub_chain = full_chain[10:20]

print "Residues in sub chain:"
for res in sub_chain.residues() : print res.fullName()

---------------------------------------------------------------

This gives:

Loading protein file
Residues in sub chain:
insulin..Cyx11
insulin..Ser12
insulin..Leu13
insulin..Tyr14
insulin..Gln15
insulin..Leu16
insulin..Glu17
insulin..Asn18
insulin..Tyr19
insulin..Cyx20

---------------------------------------------------------------


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