<div dir="ltr">Dear <span style="font-size:12.8px">Wolfram,</span><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">I'm afraid you will have to use file with parameters to do this:</span></div><div><div><span style="font-size:12.8px">modify {</span></div><div><span style="font-size:12.8px"> occupancies</span></div><div><span style="font-size:12.8px"> {</span></div><div><span style="font-size:12.8px"> atom_selection = chain A and resid 1</span></div><div><span style="font-size:12.8px"> randomize = False</span></div><div><span style="font-size:12.8px"> set = 1</span></div><div><span style="font-size:12.8px"> normalize = False</span></div><div><span style="font-size:12.8px"> }</span></div><div><span style="font-size:12.8px"> keep = not (chain A and altid B and resid 1)</span></div><div><span style="font-size:12.8px"> # or use: remove = chain A and altid B and resid 1</span></div><div><span style="font-size:12.8px">}</span></div></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">The scope "occupancies" is "multiple" which means you can have several of them. This kind of scopes cannot be populated correctly from command-line parameters. As you can see in the beginning of your set.out (in "Complete set of parameters"), you ended up with two "occupancies" scopes. The selection you provided ended up in the second scope with nothing to change, and set=1 ended up in the first scope with atom_selection=None, therefore set=1 was applied to the whole model. </span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Best regards,</span></div><div><span style="font-size:12.8px">Oleg Sobolev.</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Feb 7, 2017 at 12:19 PM, wtempel <span dir="ltr"><<a href="mailto:wtempel@gmail.com" target="_blank">wtempel@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 class="m_-5159817877086140267markdown-here-wrapper"><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-wrap;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=”<wbr>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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