<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi John,<div><span class="Apple-tab-span" style="white-space:pre"> </span>As Tim mentioned, "smart display" off is what you want. Also, "Presets->all atoms" will quickly get you a view of all atoms, though a few of them may be in sphere depiction rather than wireframe.</div><div><br></div><div>--Eric</div><div><br><div><div>On Aug 12, 2010, at 8:29 AM, Tim Travers wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello John,<div><br></div><div>What I did to configure Chimera on my Linux box was to go into Favorites->Preferences.</div><div>In the window that opens, choose New Molecules from the drop-down box Category. You</div><div> can then play with the options there; for what you need, I guess set ribbon display off,</div><div>atom style as ball, bond style as stick. And maybe also turn off the smart initial display.</div><div><br></div><div>Hope this helps,</div> <div>Tim</div><div><br><div class="gmail_quote">On Thu, Aug 12, 2010 at 11:21 AM, Beale, John <span dir="ltr"><<a href="mailto:John.Beale@stlcop.edu">John.Beale@stlcop.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"> <div bgcolor="white" background="?ui=2&ik=a3a10f3bf5&view=att&th=12a66e5af354ae62&attid=0.0.1&disp=emb&zw" lang="EN-US" link="blue" vlink="purple"><span><image001.jpg></span><div><p class="MsoNormal"><span style="font-size:11.0pt">I have a new installation of Chimera on a Linux box. I am working with a protein/nucleic acid complex. When I start the program with “chimera file.pdb” the ribbon representation of the structure is shown. Also, a plank representation of the nucleic acid is shown. I have to hide the ribbon and select “Actions -> Atoms/Bonds -> Show” to see the atoms. Can someone tell me how to change the startup options so that the ribbon and planks are not automatically generated and that the atoms/bonds are shown by default?</span></p><div><span style="font-size:11.0pt"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><span style="font-size:11.0pt">Thanks!</span></p><div><span style="font-size:11.0pt"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><span style="font-size:11.0pt">John</span></p><div><span style="font-size:11.0pt"> </span><br class="webkit-block-placeholder"></div><div><p class="MsoNormal"><b><span style="font-size:11.0pt;color:#C00000">John M. Beale, Jr., Ph.D.</span></b></p><p class="MsoNormal"><b><span style="font-size:11.0pt;color:#C00000">Professor of Medicinal Chemistry and Pharmacognosy</span></b></p><p class="MsoNormal"><b><span style="font-size:11.0pt;color:#C00000">Saint Louis College of Pharmacy</span></b></p><p class="MsoNormal"><b><span style="font-size:11.0pt;color:#C00000">4588 Parkview Place</span></b></p><p class="MsoNormal"> <b><span style="font-size:11.0pt;color:#C00000">Saint Louis, Missouri 63110</span></b></p><p class="MsoNormal"><b><span style="font-size:11.0pt;color:#C00000">314-446-8461</span></b></p><p class="MsoNormal"><b><span style="font-size:11.0pt;color:#C00000">Cell: 314-315-0409</span></b></p><p class="MsoNormal"><b><span style="font-size:11.0pt;color:#C00000">FAX: 314-446-8460</span></b></p><p class="MsoNormal"><b><span style="font-size:11.0pt"><a href="mailto:jbeale@stlcop.edu" target="_blank">jbeale@stlcop.edu</a></span></b></p> </div><div><span style="font-size:11.0pt"> </span><br class="webkit-block-placeholder"></div></div></div><br>_______________________________________________<br> Chimera-users mailing list<br> <a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br> <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br> <br></blockquote></div><br></div> _______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div></body></html>