<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Dan,<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>Chimera assumes that sp3 nitrogens bonded only to sp3 carbons and/or hydrogens are positively charged at physiological pH. That means that their idatmType attribute is "N3+". If you actually do want to use the neutral species, you need to get the idatmType changed to "N3" before adding hydrogens. Here is some Python code that will change all selected nitrogens' idatmType to "N3":</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--- start code ---</DIV><DIV>import chimera</DIV><DIV>for a in chimera.selection.currentAtoms():</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>if a.element.name != "N":</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>continue</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>a.idatmType = "N3"</DIV><DIV>--- end code ---</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>You could either type that code into the IDLE interpreter (Tools->General Controls->IDLE) or put it in a .py file and open that file with File...Open or with Chimera's command line.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV> <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>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>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="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></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> </DIV><BR><DIV><DIV>On Dec 2, 2005, at 6:53 AM, Daniel Svozil wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi all,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">if I use addH tool on the C-N, I would expect to get C-NH2, but I get<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">C-NH3 instead. How should I proceed to get C-NH2 correctly?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Dan</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Daniel Svozil, PhD</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Institute of Organic Chemistry and Biochemistry</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Center for Biomolecules and Complex Molecular Systems</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.molecular.cz/~svozil">http://www.molecular.cz/~svozil</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Czech Republic</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phone: +420-220 410 312</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>