On Fri, May 27, 2011 at 6:36 AM, Thomas C. Terwilliger <span dir="ltr">&lt;<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</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;">

I am guessing that the specification of the chain as &quot;chain B&quot; rather than<br>
as &quot;B&quot; might be the problem, but I am not certain of that.<br></blockquote><div><br></div><div>That&#39;s half of the problem - based on viewing the original email with screen captures (which the list server rejected), the other problem is that the full parameter input was this:</div>

<div><br></div><div>omit_chain_list chainB</div><div><br></div><div>I suspect there&#39;s some confusion with the command-line documentation.  You don&#39;t need to include the parameter name in the GUI, just the actual value, i.e.</div>

<div><br></div><div>chain B</div><div><br></div><div>(without quotes)</div><div><br></div><div>But I agree with Tom, running phenix.refine on a modified PDB file will be easier.  I think Pavel plans to introduce an even easier way to do this in phenix.maps at some point in the future.</div>

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