<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div dir="ltr"><span>Thank you very much. My problem is solved.</span></div><div><br></div> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div dir="ltr"> <hr size="1"> <font size="2" face="Arial"> <b><span style="font-weight:bold;">From:</span></b> Elaine Meng <meng@cgl.ucsf.edu><br> <b><span style="font-weight: bold;">To:</span></b> A Amiri <atefeh_amiri23@yahoo.com> <br><b><span style="font-weight: bold;">Cc:</span></b> "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> <br> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday, 17 September 2013, 22:08:52<br> <b><span style="font-weight: bold;">Subject:</span></b> join models C-N peptide bond<br> </font> </div>
<div class="y_msg_container"><br><div dir="ltr">Hello,<br></div><div dir="ltr">I assume you have already also chosen the "C-N peptide bond" option in Join Models and that the C is the backbone C of the last residue in a peptide chain in one model and the N is the backbone N of the first residue in a peptide chain in a different model.<br></div><div dir="ltr"><br></div><div dir="ltr">If all of the above are true, the most likely problem is that you have selected more than 2 atoms. For example, if you just select on the ribbon with the mouse, it selects the whole residue, not just an atom in the residue. You can see how many atoms you have selected by clicking the green magnifying glass near the bottom right corner of the Chimera window. The resulting dialog will show how many atoms are selected.<br></div><div dir="ltr"><br></div><div dir="ltr">To select only two atoms, display atoms instead of ribbons and then use the mouse to select
them. For example, to show only peptide backbone atoms, you could use commands:<br></div><div dir="ltr"><br></div><div dir="ltr">~ribbon<br></div><div dir="ltr">show protein & @n,ca,c,o<br></div><div dir="ltr"><br></div><div dir="ltr">The selection could be done with the mouse (Ctrl-click on one atom, Shift-Ctrl-click on the other) or with commands, for example:<br></div><div dir="ltr"><br></div><div dir="ltr">sel #0:<a ymailto="mailto:368.A@C" href="mailto:368.A@C">368.A@C</a> #1:<a ymailto="mailto:1.A@N" href="mailto:1.A@N">1.A@N</a><br></div><div dir="ltr"><br></div><div dir="ltr">(of course, the exact command would depend on the residue numbers and chain IDs in your structures)<br></div><div dir="ltr">I hope this helps,<br></div><div dir="ltr">Elaine<br></div><div dir="ltr">----------<br></div><div dir="ltr">Elaine C. Meng, Ph.D. <br></div><div dir="ltr">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></div><div
dir="ltr">Department of Pharmaceutical Chemistry<br></div><div dir="ltr">University of California, San Francisco<br></div><div dir="ltr"><br></div><div dir="ltr">On Sep 17, 2013, at 2:44 AM, A Amiri <<a ymailto="mailto:atefeh_amiri23@yahoo.com" href="mailto:atefeh_amiri23@yahoo.com">atefeh_amiri23@yahoo.com</a>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">> Hello.<br></div><div dir="ltr">> I have a problem with chimera! i want to join two pdb file together by C-N peptide bond. Actually this is a modeling of a fusion protein that one part of its, is a protein and another part is a linker. I need a complete structure.<br></div><div dir="ltr">> I select the carbon atom from one model and nitrogen atom from another model. I use the "build structure<join modesl" menu for this purpose but the "apply" button is inactive still and i don't know how i can activate it!<br></div><div dir="ltr">> please help
me.<br></div><br><br></div> </div> </div> </div></body></html>