<html>
<head>
<style>
body {
font-family: Verdana, sans-serif;
font-size: 0.8em;
color:#484848;
}
h1, h2, h3 { font-family: "Trebuchet MS", Verdana, sans-serif; margin: 0px; }
h1 { font-size: 1.2em; }
h2, h3 { font-size: 1.1em; }
a, a:link, a:visited { color: #2A5685;}
a:hover, a:active { color: #c61a1a; }
a.wiki-anchor { display: none; }
fieldset.attachments {border-width: 1px 0 0 0;}
hr {
width: 100%;
height: 1px;
background: #ccc;
border: 0;
}
span.footer {
font-size: 0.8em;
font-style: italic;
}
</style>
</head>
<body>
Issue #2780 has been updated by Lenna Peterson.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15368?detail_id=1671">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Resolved</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>Migrated to github:</p>
<p><a class="external" href="https://github.com/biopython/biopython/issues/991">https://github.com/biopython/biopython/issues/991</a></p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2780#change-15368">Bug #2780: PDB file HETATMs cannot be alternative location of a residue that is an ATOM</a></h1>
<ul><li>Author: Klaus Kopec</li>
<li>Status: Resolved</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: 1.50</li>
<li>URL: </li></ul>
<p>In PDB files where HETATMs and ATOMs are altlocs of each other (e.g. 1RR2, residue 184), they are treated as two separate residues.</p>
<p>A obvious solution is to add an "else" case to the "if" in StructureBuilder.py line 115 (method init_residue(...)) that introduces some kind of mixed (HETATM as well as ATOM) DisorderedResidue.</p>
<p>The Main problem with that: the hetero field of the residue ids will differ between the residues, therefore the whole access-over-ids mechanism will most likely not work with these MixedDisorderedResidues as straight forward as it does so far.</p>
<p>Sadly, I could not come up with a good solution for this. Maybe some <i>getattr</i> magic that alters the way Chains access their residues might work by allowing access to residues by only using the second and third component of the id 3-tuple?!</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1256/1rr2_residues184AB.pdb">1rr2_residues184AB.pdb</a>
(1.66 KB)<br />
</fieldset>
<hr />
<span class="footer"><p>You have received this notification because you have either subscribed to it, or are involved in it.<br />To change your notification preferences, please click here and login: <a class="external" href="http://redmine.open-bio.org">http://redmine.open-bio.org</a></p></span>
</body>
</html>