<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Atsutoshi,<DIV>If you want the "element" coloring (oxygen red, nitrogen blue, ... ) one way is to use the menu item:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Actions... Color... by element</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Actually there are many different ways to color atoms, ribbons, surfaces, and other things. The many ways are listed in this manual page:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><A href="http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/coloring.html">http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/coloring.html</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>In Chimera, you can search for help using the menu item:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Help... Search Documentation</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>for example, if you search by "coloring" the page I mentioned above is hit #2. There are also tutorials for new users of Chimera (Help... Tutorials).</DIV><DIV>I hope this helps,</DIV><DIV>Elaine</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV><DIV>On Oct 23, 2006, at 10:28 PM, Atsutoshi Okabe wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <DIV class="Section1" style="layout-grid:18.0pt"><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN lang="EN-US" style="font-size: 10.0pt;font-family:Arial">Hi,<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN lang="EN-US" style="font-size: 10.0pt;font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN lang="EN-US" style="font-size: 10.0pt;font-family:Arial">I visualized one ligand molecule (a kind of sugar) written by PDB format within chimera.<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN lang="EN-US" style="font-size: 10.0pt;font-family:Arial">But all atoms have non color(attached file ) I want to color these atoms (i.e. the oxygen has red …)<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN lang="EN-US" style="font-size: 10.0pt;font-family:Arial">Could you please teach me how to color atoms?<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN lang="EN-US" style="font-size: 10.0pt;font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Century"><SPAN lang="EN-US"><O:P> </O:P></SPAN></FONT></P> </DIV> <SPAN><DIV><ligand.jpg></DIV></SPAN><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> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; "><DIV>-----</DIV><DIV>Elaine C. Meng, Ph.D. <A href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</A></DIV><DIV>UCSF Computer Graphics Lab and Babbitt Lab</DIV><DIV>Department of Pharmaceutical Chemistry</DIV><DIV>University of California, San Francisco</DIV><DIV> <A href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></BODY></HTML>