<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><DIV>On Nov 6, 2007, at 7:38 AM, Greg Pintilie wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">yes, try:</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 14.0px Monaco; min-height: 19.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">chimera.selection.currentAtoms()</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 14.0px Monaco; min-height: 19.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">this will return a list of the currently selected atoms in the Chimera viewer.</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 14.0px Monaco; min-height: 19.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 14.0px Monaco; min-height: 19.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">For your purposes, it sounds like you want vectors between every two</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">atoms that you subsequently select. Watch out however, that the list</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">returned by the above command need not be in the order that you made</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">the selection. I noticed that in general the selection routines return</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">atoms in arbitrary order, independent of the selection order or their</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">position in the structure. Not sure if there is any way to enforce any</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">kind of order?</FONT></P> </BLOCKQUOTE><BR></DIV><DIV>chimera.selection.currentAtoms(ordered=True)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>This returns the atoms in the order they were selected. It's not the default since it involves a possibly-expensive sorting operation and because many uses of the current selection don't care about the ordering.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> <SPAN class="Apple-converted-space"> </SPAN></SPAN>Eric Pettersen</FONT></P><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> <SPAN class="Apple-converted-space"> </SPAN></SPAN>UCSF Computer Graphics Lab</FONT></P><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></BODY></HTML>