<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Jared,<DIV>Currently you cannot bond different models, and the only way to "merge" is to put the atoms in the same file before opening it. There are actually other reasons your command wouldn't work:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>- seems to me that there is no model 1, only 1.1, 1.2, 1.3 and 1.4, so the first part would specify zero atoms</DIV><DIV>- the ampersand & stands for intersection (logical AND, not english and) and should be omitted, e.g.</DIV><DIV> command: bond #1.1:504.b@c #1.1:505.b@n</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>What I've done in the past to handle similar cases (splicing stuff from an NMR structure onto a Xray structure) is to first put the tail (with a few extra residues to overlap with residues that are already present) into a file by itself. Then I open that new file, so it will be a new, separate model. I then match that model onto the original model using atoms in the overlapping part. Then, write out another PDB file of the tail relative to the untransformed original model. Using text-editing, remove the part that overlaps since it was just there for positioning purposes. FINALLY (text-editing again) make another PDB file that combines the new tail with the original protein. They may need to have the same chain ID as well. Sorry this is such a long process. If you think you can hand-position the tail sufficiently well you could skip the parts about having the extra atoms, using them for matching, and deleting them.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>If you remove any intervening TER, the bond will already be there when you open the new file.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I hope this helps,</DIV><DIV>Elaine</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV><DIV>On Sep 28, 2006, at 10:13 AM, Jared Godar wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">I have an incomplete pdb crystal structure of a homohexameric protein containing six ~25AA tails. In the incomplete model, two of these six tails are complete (A and F) and the other four are truncated at various positions (B,C,D, and E). I have used the either the A or F complete tails as templates and generated appropriate length segments to compleate each of the truncated B-E tails by selecting the appropriate residues and saving the selected atoms as a new PDB. Currently, I have all six tails completed and saved as a single PDB. I would like to use the Bond command to covalently link the extended chains, but my single PDB is segregated into models 1.1, 1.2, 1.3, 1.4, and 1.5. When I use the Bond command as follows "bond #1:504.b@c & #1.3:505.a@n", I get an error that only one atom is selected. Does Chimera consider #1 and #1.1 to be different models? If so, how can I merge these 5 models into one to allow me to create the bond?<BR> <BR> Thanks,<BR> <BR> Jared<BR clear="all"><BR>-- <BR>Jared A. Godar<BR>Graduate Student: Stewart Lab<BR>Vanderbilt University Medical Center<BR>Department of Molecular Physiology & Biophysics<BR>708 Light Hall <BR>2215 Garland Ave.<BR>Nashville, TN 37232-0615 <BR>Work: 615.322.7898<BR>Fax: 615.322.7236<BR><BR><A href="mailto:jared.godar@vanderbilt.edu">jared.godar@vanderbilt.edu</A><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>