<div dir="ltr">This doesn't exactly answer your question, but you can get them via FTP, e.g:<div><div><a href="ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates/divided/hr/1hri.pdb1.gz">ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates/divided/hr/1hri.pdb1.gz</a><br></div><div><br></div><div>This file contains 60 models (one for each of the BIOMTX matrices in the original PDB file). Helpfully, biopython knows how to handle multiple models, so just download, unzip and read that in</div><div><a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec162">http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec162</a><br></div><div><br></div><div><br></div><div>Fred</div><div><br></div><div><br></div><div>ps. If you want to understand how it works, or write your own code to do it:</div><div><br></div><div>You use the BIOMT records to create a series of 3x3 matrices. e.g. these three lines from the PDB file correspond to one transformation:</div><div><div><br></div><div><font face="monospace">REMARK 350 BIOMT1 2 0.500000 -0.809017 0.309017 0.00000 </font></div><div><font face="monospace">REMARK 350 BIOMT2 2 0.809017 0.309017 -0.500000 0.00000 </font></div><div><font face="monospace">REMARK 350 BIOMT3 2 0.309017 0.500000 0.809017 0.00000 </font> </div></div><div><br></div><div>use these to make a matrix</div><div><br></div><div><font face="monospace">>>> import numpy as np</font></div><div><div><font face="monospace">>>> m = np.array([[ 0.5, -0.809017, 0.309017],</font></div><div><font face="monospace"> [ 0.809017, 0.30917, -0.5 ],</font></div><div><font face="monospace"> [ 0.309017, 0.5, 0.809017]])</font></div></div><div><br></div><div>Then for each coordinate in your original PDB, e.g. the first one:</div><div><div><font face="monospace">>>> a = np.array([35.887, 31.402, 96.395])</font></div></div><div><br></div><div>take the dot product:</div><div><font face="monospace">>>> np.dot(m,a)</font></div><div><div><font face="monospace">array([ 22.32644188, -9.45575058, 104.77588679])</font></div></div><div><br></div><div>You'll see these coordinates correspond to the first line of model 2 in the biological assembly file I linked above (line 6480)</div><div><br></div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 13 November 2014 06:50, Bhushan <span dir="ltr"><<a href="mailto:nagbiotech1@gmail.com" target="_blank">nagbiotech1@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>Hi,<br><br></div><div>I want to apply the symmetry matrix on pdb 1HRI and output the biological assembly (with rotated coordinates). Can anyone suggest me a way to do this using biopython.<br><br></div><div>Thank you for your time. I would appreciate any kind of help.<br><br><br></div><div>With Regards,<br>Bhushan.<br></div></div>
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