<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks to you both.<div><br></div><div>The excellent functionality of Chimera is only surpassed by the extraordinary support you give your users. </div><div><br></div><div>We REALLY appreciate it!</div><div><br></div><div>Jim </div><div><br><div><div>On Oct 14, 2008, at 4:06 PM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>On top of Elaine's good suggestions, there's a horrible kludge that you could possibly use. Before you open your additional structure, save a session. Then open your new structure, position it, and close the other models. Apply your preset. Restore the session you saved and when Chimera asks you if you want to close existing models say no.<br><br>--Eric<br><br>On Oct 14, 2008, at 12:49 PM, Elaine Meng wrote:<br><br><blockquote type="cite">Hi Jim,<br></blockquote><blockquote type="cite">Presets always act on everything; they include global settings (e.g.<br></blockquote><blockquote type="cite">background color) and adjust depending on what structures are present<br></blockquote><blockquote type="cite">(different results for one chain vs. multiple chains in one model vs.<br></blockquote><blockquote type="cite">multiple models).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">However, presets are just multiple steps rolled into one for your<br></blockquote><blockquote type="cite">convenience. You can perform the desired steps on models selectively<br></blockquote><blockquote type="cite">using the Actions menu and/or commands. If you first select the<br></blockquote><blockquote type="cite">model, the Actions menu items will apply only to that model: hiding<br></blockquote><blockquote type="cite">atoms, showing ribbon, changing ribbon style to smooth, etc. With<br></blockquote><blockquote type="cite">commands, you can specify what you want to do (verb) and what you want<br></blockquote><blockquote type="cite">to do it to (subject) all in one. The descriptions of the presets<br></blockquote><blockquote type="cite">will give you some information on what they comprise, but feel free to<br></blockquote><blockquote type="cite">write back if you have trouble identifying the needed menu item or<br></blockquote><blockquote type="cite">command.<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">A related feature you might not know about is the "New Molecules"<br></blockquote><blockquote type="cite">category within Preferences (Favorites... Preferences). You can<br></blockquote><blockquote type="cite">specify how you want structures to appear when first opened (remember<br></blockquote><blockquote type="cite">to click Save if you want settings to apply to later uses of<br></blockquote><blockquote type="cite">Chimera). This panel is not complete, however... for example, there<br></blockquote><blockquote type="cite">is no option to undisplay the atoms.<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules</a><br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">see also the "New Surfaces" category:<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfaces">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfaces</a><br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Yet another possibility is to make a command alias that does all your<br></blockquote><blockquote type="cite">favorite things,<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">For example, start chimera, show the Command Line (Favorites...<br></blockquote><blockquote type="cite">Command Line) and try the commands:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">alias makenice ~disp $1; ribbon $1; ribrep smooth $1; col byhet $1;<br></blockquote><blockquote type="cite">rep stick $1; disp $1 & ligand z<4<br></blockquote><blockquote type="cite">open 2gbp<br></blockquote><blockquote type="cite">open 1zik<br></blockquote><blockquote type="cite">preset apply int 1<br></blockquote><blockquote type="cite">open 2mnr<br></blockquote><blockquote type="cite">makenice #2<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">(** that alias command should be all one line even though the annoying<br></blockquote><blockquote type="cite">mail program will probably insert a return **)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">That opens 2gbp as model #0, 1zik as #1, and 2mnr as #2. Since #2 was<br></blockquote><blockquote type="cite">opened after the preset was used, it can be adjusted without affecting<br></blockquote><blockquote type="cite">the other models by way of the alias "makenice".<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Aliases are saved in sessions. You could even make a command file<br></blockquote><blockquote type="cite">with that alias command in it and simply open the command file in<br></blockquote><blockquote type="cite">different Chimera sessions to create the alias.<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile</a><br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In the Model Panel, "active" means movable, such as with the mouse or<br></blockquote><blockquote type="cite">movement commands such as "move":<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I hope this helps,<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite">-----<br></blockquote><blockquote type="cite">Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></blockquote><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote><blockquote type="cite">University of California, San Francisco<br></blockquote><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Oct 14, 2008, at 11:07 AM, James Nettles wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Something that often comes up is that I have some number of aligned<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">protein structures with nicely color coded secondary features and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">specific side chains. I then want to fit another molecule in this<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">same space and apply a "preset" graphic mode to the new structure<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">without undoing the previous molecular views.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I expect this is possible, but I haven't gotten it to work yet. I've<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">tried making only my molecule of interest "active" in the Model<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Panel, but the preset still effects everything.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I'm using Alpha build 2557 2008/09/13 at the moment.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Jim<br></blockquote></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Chimera-users mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></blockquote><br><br></div></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; 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; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">________________________________________________________</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">James Nettles, Ph. D. Assistant Professor </font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Department of Pediatrics, Emory University School of Medicine</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Laboratory of Biochemical Pharmacology (LOBP)</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Computer Assisted Discovery Research Environment (CADRE)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">________________________________________________________</div><div><br></div></div></div><div><br></div></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>