On Mon, Jun 21, 2010 at 12:49 PM, S. Saif Hasan <span dir="ltr">&lt;<a href="mailto:sshasan@purdue.edu">sshasan@purdue.edu</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 have a membrane protein complex made up of 8 different polypeptides present in<br>
two copies each (16mer). The asymmetric unit is the octamer, as determined from<br>
previous crystallographic studies. To carry out molecular replacement with the<br>
phases from the published structure in AutoMR, should I specify the coordinates<br>
of the search model and its overall sequence identity as one file or should I<br>
break it down for each subunit ?</blockquote><div><br></div><div>If it doesn&#39;t have any large conformational changes, using the entire octamer might work.  It will certainly be much faster than placing each chain separately, so it&#39;s worth trying first anyway.  You should run rigid-body refinement afterwards with a rigid group for each chain.  If you can&#39;t place the octamer, try searching for smaller sub-assemblies before you break it down into individual chains.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Also, for the asymmetric unit contents, should<br>
I specify the sequence or mass of each subunit separately (as component 1, 2 and<br>
so on) keeping the number of copies fixed at 1 ? There is no NCS.<br></blockquote><div><br></div><div>I think you can just specify the overall mass - regardless of whether you&#39;re searching for the entire complex or one chain at a time.</div>
<div><br></div><div>-Nat</div></div>