<div dir="ltr"><div>Joao,<br><br></div>I'm quite sure you are not suggesting to change the co-ordinates "manually" i.e. one by one like in a text file. I'm writing some code to do that. Also, I am yet to check out Patrick Kunzmann's code. I think Patrick's code would do a great job.<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 6:54 PM, João Rodrigues <span dir="ltr"><<a href="mailto:j.p.g.l.m.rodrigues@gmail.com" target="_blank">j.p.g.l.m.rodrigues@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">Meanwhile, the way to do it is to go over all the atoms again and change their xyz coordinates manually.</div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2017-05-23 4:01 GMT-07:00 Souparno Adhikary <span dir="ltr"><<a href="mailto:souparnoa91@gmail.com" target="_blank">souparnoa91@gmail.com</a>></span>:<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_-182332765760807118m_-4537656661817331516gmail_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="m_-182332765760807118h5">
<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">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_-182332765760807118m_-4537656661817331516m_-8833725069458260617moz-txt-link-freetext" href="https://github.com/padix-key/biopython/tree/numpy-structure" target="_blank">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_-182332765760807118m_-4537656661817331516h5">
    <br>
    <div class="m_-182332765760807118m_-4537656661817331516m_-8833725069458260617moz-cite-prefix">Am 23.05.2017 um 12:04 schrieb Souparno
      Adhikary:<br>
    </div>
    </div></div><blockquote type="cite"><div><div class="m_-182332765760807118m_-4537656661817331516h5">
      <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_-182332765760807118m_-4537656661817331516m_-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>
      <br>
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      <br>
      </div></div><pre>______________________________<wbr>_________________
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    </blockquote>
    <br>
  </div>

</blockquote></div><br></div></div></div></div>
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