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<p>Using my subpackage, this might work for you:</p>
<p>import Biopython.Bio.Structure as struc<br>
from Bio.PDB import PDBParser<br>
from Bio.PDB import PDBIO<br>
from Bio.PDB.Structure import Structure<br>
<br>
parser = PDBParser(PERMISSIVE=True)<br>
structure = parser.get_structure("", "1l2y.pdb")<br>
stack = struc.stack([struc.to_array(model) for model in
structure])<br>
average_atom_array = struc.average(stack)<br>
structure_new = Structure("result")<br>
structure_new.add(struc.to_model(average_atom_array))<br>
io = PDBIO()<br>
io.set_structure(structure_new)<br>
io.save("result.pdb")<br>
</p>
<br>
<div class="moz-cite-prefix">Am 23.05.2017 um 13:03 schrieb Souparno
Adhikary:<br>
</div>
<blockquote type="cite"
cite="mid:CAL6QJ1CeKeBJamCimSTasEu6BWwzJnhaTVycqzvPFQACFSns3w@mail.gmail.com">
<div dir="ltr">Oh, got it. It's only a dot problem.<br>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div>
<div>Souparno Adhikary,<br>
</div>
CHPC Lab,<br>
</div>
Department of Microbiology,<br>
</div>
University of Calcutta.<br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Tue, May 23, 2017 at 4:31 PM,
Souparno Adhikary <span dir="ltr"><<a
href="mailto:souparnoa91@gmail.com" target="_blank"
moz-do-not-send="true">souparnoa91@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>The page shows a 404 error. Can you please check the
link again?<br>
<br>
</div>
Regards,<br>
<div class="gmail_extra"><br clear="all">
<div>
<div class="m_-4123146997538492146gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div>
<div>Souparno Adhikary,<br>
</div>
CHPC Lab,<br>
</div>
Department of Microbiology,<br>
</div>
University of Calcutta.<br>
</div>
</div>
</div>
<div>
<div class="h5">
<br>
<div class="gmail_quote">On Tue, May 23, 2017 at
4:01 PM, Patrick Kunzmann <span dir="ltr"><<a
href="mailto:padix.kleber@gmail.com"
target="_blank" moz-do-not-send="true">padix.kleber@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>I am currently working on a subpackage for
Biopython (called Bio.Structure), that
converts a Bio.PDB.Model.Model into a numpy
array containing coordinates and annotations
for doing easily efficient calculations (for
example calculating average structure). This
array can be converted back into a
Bio.PDB.Model.Model and than saved as PDB
file using PDBIO(). Currently docstrings and
code comments are missing, so I will
contribute this code only in a few days, but
you can check out the source code at <a
class="m_-4123146997538492146m_-8833725069458260617moz-txt-link-freetext"
href="https://github.com/padix-key/biopython/tree/numpy-structure"
target="_blank" moz-do-not-send="true">https://github.com/padix-key/b<wbr>iopython/tree/numpy-structure</a>.</p>
<p>Best regards,</p>
<p>Patrick Kunzmann<br>
</p>
<div>
<div class="m_-4123146997538492146h5"> <br>
<div
class="m_-4123146997538492146m_-8833725069458260617moz-cite-prefix">Am
23.05.2017 um 12:04 schrieb Souparno
Adhikary:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="m_-4123146997538492146h5">
<div dir="ltr">
<div>
<div>
<div>I want to calculate the
average structure from multiple
frames in a pdb file and save it
to another pdb file.<br>
<br>
</div>
I wrote the code to calculate the
average co-ordinates successfully
like below:<br>
<br>
#!/usr/bin/python<br>
<br>
from Bio.PDB.PDBParser import
PDBParser<br>
<br>
import numpy as np<br>
<br>
parser=PDBParser(PERMISSIVE=1)<br>
<br>
structure_id="mode_7"<br>
filename="mode_7.pdb"<br>
structure=parser.get_structure<wbr>(structure_id,
filename)<br>
model1=structure[0]<br>
s=(124,3)<br>
newc=np.zeros(s,dtype=np.float<wbr>32)<br>
counter=1<br>
fincoord=[]<br>
for i in range(0,29):<br>
coord=[] <br>
model=structure[i]<br>
for chain in model.get_list():<br>
for residue in
chain.get_list():<br>
ca=residue["CA"]<br>
coord.append(ca.get_coord())<br>
<br>
newc=np.add(newc,coord)<br>
counter+=1<br>
<br>
fincoord=np.divide(newc,counte<wbr>r)<br>
<br>
print fincoord<br>
<br>
print "END"<br>
<br>
</div>
Now I want to write the coordinates
in fincoord to a new pdb file i.e.
everything will be the same like the
structure[0] except the coordinates.
Can you tell me how can I edit the
coordinates of a specific model or
replace it with my array and save it
to another file?<br>
<br>
</div>
Thanks<br clear="all">
<div>
<div>
<div>
<div>
<div>
<div
class="m_-4123146997538492146m_-8833725069458260617gmail_signature">
<div dir="ltr"><br>
</div>
<div>Souparno Adhikary,<br>
</div>
<div>CHPC Lab,<br>
</div>
<div>University of
Calcutta.<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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