<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Virginia,<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>The Selector Construction panel could probably stand some interface improvements for sure. "Existing Selection" has nothing to do with what's selected in the Chimera window as you construct the selector. "Existing Selection" grabs whatever is selected in the Chimera window when the selector is used (either by choosing the selector from Chimera's Select menu, of invoking it from the Select region of the construction panel) -- so it can be a different selection every time it is used. Anyway, you can ignore that because it doesn't really help you with your problem.</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>There is no easy way to select all lysines within 8 angstroms of another lysine in Chimera, so you were on the right track with trying to construct a selector, but it requires actually putting some custom Python code in your selector since you need to loop over lysine residues individually in order to get what you want. So open the Selector Construction panel, pick "Show workbench selector contents" in the Panels menu, and paste in:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>from chimera import specifier</DIV><DIV>sel.merge(selection.REPLACE, specifier.evalSpec(":LYS"))</DIV><DIV>nearRes = []</DIV><DIV>sel2 = selection.ItemizedSelection()</DIV><DIV>for r in sel.residues():</DIV><DIV> sel2.clear()</DIV><DIV> sel2.add(r)</DIV><DIV> sel2.merge(selection.REPLACE, specifier.zone(sel2, specifier.ATOM, None, 8.0, models))</DIV><DIV> selRes = [sr for sr in sel2.residues() if sr.type == "LYS"]</DIV><DIV> selRes.remove(r)</DIV><DIV> nearRes.extend(selRes)</DIV><DIV>sel.clear()</DIV><DIV>sel.add(nearRes)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Since the remailer for this list may break long lines, I've also attached the above as a file. If you are using the X11 version of Chimera for the Mac, pasting in the text is tricky -- if you're using that let me know and I can send instructions about how to get the pasting to work.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV></DIV></BODY></HTML>