<p dir="ltr">Hi Rojan, </p>
<p dir="ltr">The code looks o.k. to me. Waters are sometimes in ATOM records, which would break the parser. </p>
<p dir="ltr">Another reason can be that you are iterating and removing the waters at the same time. Try saving the ids of the heteroatoms you want to remove to a, list and then iterate over this list and remove them. </p>
<p dir="ltr">Best, <br>
João </p>
<div class="gmail_quote">Em 05/09/2014 07:21, "Rojan Shrestha" <<a href="mailto:rojan@riken.jp">rojan@riken.jp</a>> escreveu:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>Hello,</div><div><br></div><div>Can someone tell me about removing heteroatoms from PDB?</div><div><br></div><div>Here is the code for removing the heteroatoms I took from the link - <a href="http://pelican.rsvs.ulaval.ca/mediawiki/index.php/Manipulating_PDB_files_using_BioPython" target="_blank">http://pelican.rsvs.ulaval.ca/mediawiki/index.php/Manipulating_PDB_files_using_BioPython</a> but it did not work. I have tested with 1C4R.pdb. It removes some water but some still remain in PDB.</div><div><pre style="font-family:monospace,Courier;padding:1em;border:1px dashed rgb(47,111,171);background-color:rgb(249,249,249);line-height:1.1em;font-size:13px">for model in structure:
for chain in model:
for residue in chain:
id = <a href="http://residue.id" target="_blank">residue.id</a>
if id[0] != ' ':
chain.detach_child(id)
if len(chain) == 0:
model.detach_child(<a href="http://chain.id" target="_blank">chain.id</a>)</pre></div><div><br></div><div>Regards,</div><div><br></div><div>Rojan </div></div>
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