<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Enrico,<div><span class="Apple-tab-span" style="white-space:pre"> </span>As Elaine pointed out, you can't form a covalent bond between two models (since that's the definition of "model" in Chimera). Forming a pseudobond as Elaine outlines is one possibility. The other alternative is to combine the two models into one by using the "combine" command or the "copy/combine" button of the Model Panel. Once you have a single model you can then use the "bond" command to form a bond between the atoms.</div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span>However, I recommend Elaine's approach unless there's a specific reason you need a single model (such as writing out a PDB file without MODEL records).</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <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; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><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"></div></span> </div><br><div><div>On May 18, 2009, at 9:38 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Enrico,<br>Chimera doesn't allow adding a bond between two different models <br>(structures opened from two different files), but if you mainly want <br>the appearance of a bond, you can create a "pseudobond" connecting the <br>atoms.<br><br>Pseudobonds are just lines drawn between any pair of atoms. You can <br>control their style, thickness, color, and labels. To make <br>pseudobonds, create a text file where each line gives the two atoms to <br>be connected, and the desired color and optional label. In your case <br>the file might be only one line. Then use the Pseudobond Reader tool <br>to open the text file and create the pseudobond(s). Here is the <br>description of that tool and the file format:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html</a> <br><blockquote type="cite"><br></blockquote><br>For further changes such as line style and color, open Pseudobond <br>Panel (under Tools... General Controls), and in that dialog choose <br>your pseudobonds on the left side and click the "attributes..." button <br>on the right. That will bring up another window with options to <br>adjust the display. Such changes could also be done with the <br>"setattr" command, but it is trickier. You may want to make your new <br>pseudobond look the same as other metal complex pseudobonds (default <br>medium purple, linewidth 2.5, dashed)<br><<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 type="cite"><br></blockquote><br>Currently there is no command to add pseudobonds. You could make the <br>pseudobond ahead of time and undisplay it, then show it later within a <br>script, using the "setattr" command:<br><br>setattr p display false ions z<4<br>setattr p display true ions z<4<br><br>where the "ions z<4" part limits the effect to only pseudobonds around <br>ions. I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br><br>On May 18, 2009, at 8:22 AM, Enrico Morelli wrote:<br><br><blockquote type="cite">Dear all,<br></blockquote><blockquote type="cite">We would like to know if is it possible, when we have two molecules<br></blockquote><blockquote type="cite">docked together, to form a coordination bond between a metal ion<br></blockquote><blockquote type="cite">present in one of the two molecules and a donor atom of the<br></blockquote><blockquote type="cite">other molecule, in such way forming a covalent bond between the two<br></blockquote><blockquote type="cite">proteins.<br></blockquote><blockquote type="cite">Thanks<br></blockquote>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></div></body></html>