<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BLOCKQUOTE type="cite"></BLOCKQUOTE><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>Thanks to all who replied.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>And thank you Ralf for your suggestion (quoted below), this worked very nicely!</DIV><DIV>Somehow I missed this possibility in the online documentation.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>To reply to Pavel's question regarding how I figured out that tris is present at 1/2 occupancy:</DIV><DIV>(1) density was first modelled with waters but they were too close together, and there was a fairly clear tetrahedral shape.</DIV><DIV>(2) phosphate didn't refine well -- lead to huge negative difference peak at the P atom.</DIV><DIV>(3) only other tetrahedral shape molecule in the soup was tris (TAM), and after refining just the tetrahedral core it was possible to see where the three arms extended.</DIV><DIV>(4) b-factors for the tris were high relative surrounding protein atoms, and extraneous density suggested two alternate conformations for the nearby arg side-chain, one of which is too close to realistically exist next to the tris ligand. the other clue was that trial occupancy refinement of all atoms put most tris atoms in the 0.4-0.6 occupancy range.</DIV><DIV>(5) tris with 0.5 occupancy, arg with two alt confs, plus a few waters at 0.5 occupancy is so far the best model with no significant different densities for this region.</DIV><DIV>(6) the modelling will need to be confirmed with an SA omit ...</DIV><DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">Hi Cathy,</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">> The density suggests that when tris is not there,</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">> a side chain moves very close to that position</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">You could model this with alternative conformations. If you assign</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">"altloc" A and B to two conformers of your protein, and just, say, B</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">to your TAM, then the ligand would only "see" your B protein. If you</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">don't define the B conformer (no atoms) then TAM wouldn't see that</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">part of the protein at all.</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">Actually, this approach seems better to me than working with</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">atom selections.</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">Ralf</SPAN></FONT></DIV></BLOCKQUOTE><BR></DIV></BODY></HTML>