On Fri, May 27, 2011 at 6:36 AM, Thomas C. Terwilliger <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>></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 "chain B" rather than<br>
as "B" might be the problem, but I am not certain of that.<br></blockquote><div><br></div><div>That'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's some confusion with the command-line documentation. �You don'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>