Question: Extract all the residues of chain A between the z coordinate (-14.000 to 14.000)
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gravatar for Satish
7 months ago by
Satish0
Satish0 wrote:

Hello !! I want to process several pdb files.I am using pdb file from OPM database.It has the orientation of proteins in the membrane.The membrane region in pdb file is marked with dummy atom 'DUM'.I want to extract all the protein Atoms of chain A in the membrane region.Along with the dummy atoms.I am stuck in doing both.I would appreciate if i get a guidance and help.

lines = open('1fx8.pdb').readlines()

outlines = ''

for line in lines:

  if line.startswith('ATOM') and line[22] == 'A' and (line[47:54] >= -14.800 or line[47:54] <= 14.800):
    outlines += line

outfile = open('ChainA_1fx8.pdb', 'w')

outfile.write(outlines)

outfile.close()

pdb file sequence • 163 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by Satish0
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