On Mon, Nov 12, 2012 at 5:08 AM, Antony Oliver <span dir="ltr">&lt;<a href="mailto:Antony.Oliver@sussex.ac.uk" target="_blank">Antony.Oliver@sussex.ac.uk</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

Apologies if this has been covered before - but can someone point me to a way of renumbering only specific chains (i.e. F, G, H etc).<br>
I have tried using phenix.pdbtools with either selection = &quot;chain F or chain G or chain H&quot; or keep &quot;chain A or chain B or chain C or chain D&quot; - but in both cases phenix renumbers every single residue!<br>

</blockquote><div><br></div><div>If you don&#39;t mind doing it interactively, try this:</div><div><br></div><div>phenix.pdb_editor</div><div><br></div><div>(also in the GUI, of course)  Still in development, but it&#39;s meant to be used for situations like this.  The big drawback of course is that you can&#39;t script it.</div>

<div><br></div><div>Otherwise, what you&#39;re describing is very easy to code in Python, but it looks like pdbtools is simply not implemented this way.  One of us can change that (and possibly send you a patch, if it doesn&#39;t end up being too complex).</div>

<div><br></div><div>-Nat</div></div>