<div dir="ltr"><div class="markdown-here-wrapper" style=""><p style="margin:1.2em 0px!important">Hello all,<br>suppose I would like to remove one alternate conformation B from residue 1 in chain A and set the occupancy of remaining atoms in that residue to 1.</p>
<p style="margin:1.2em 0px!important"></p><pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline;white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important">phenix.pdbtools alts_minim.pdb occupancies.set=1 \<br>  occupancies.atom_selection=”chain A and resid 1” \<br>  keep=”not (chain A and altid B and resid 1)” \<br>  output.file_name=alts.out.pdb</code></pre><br>There are better methods to achieve that, but I eventually would like to expand this command to do other “things” to my coordinates.<br>Well, so far I have failed to have the <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline">atom_selection</code> to work the way <em>I</em> expect. stdout reveals that the program fails to apply a common scope to the command switches, and proceeds to reset occupancies of all atoms. Can this be done on the command line? A minimal (not) working example is attached, and your feedback appreciated.<br>Best regards.<br>Wolfram Tempel<p style="margin:1.2em 0px!important"></p>
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