<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Yangqi<div class="">Even though it is often included in the PDB file HELIX lines, Chimera does not automatically tag different kinds of helix. They are all lumped together in “helix”</div><div class=""><br class=""></div><div class="">Although it is not very convenient, to find out which residues are in 3-10 helices in many deposited structures, you can look in the PDB file text for the HELIX lines, and then see the number in column 40 as described here (“1” is right-handed alpha, “5” is right-handed 3-10, etc.):</div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary</a>></div><div class=""><br class=""></div><div class="">For example, I see that 3KK4 has several 3-10 helices by looking in the text of its PDB file. Looking at chain A only, the HELIX lines are:</div><div class=""><br class=""></div><div class=""><font face="Courier" class="">HELIX 1 1 ASN A -1 ARG A 7 1 9<br class="">HELIX 2 2 ASN A 9 TYR A 13 5 5<br class="">HELIX 3 3 GLN A 33 ASP A 46 1 14<br class="">HELIX 4 4 ARG A 49 GLY A 66 1 18<br class="">HELIX 5 5 ASN A 70 GLU A 88 1 19<br class="">HELIX 6 6 PRO A 98 LEU A 102 5 5<br class="">HELIX 7 7 ASP A 103 ARG A 109 1 7<br class="">HELIX 8 8 PRO A 112 TYR A 116 5 5</font></div><div class=""><br class=""></div><div class="">That means chain A residues 9-13, 98-102, and 112-116 were identified as 3-10 helix. </div><div class=""><br class=""></div><div class="">If you wanted to use that information, you could (for example) make an alias for that set of residues for convenience in later commands, or just specify them directly, say</div><div class=""><br class=""></div><div class="">open 3kk4</div><div class="">delete ~ :.a</div><div class="">alias tthel :9-13,98-102,112-116</div><div class="">color red tthel</div><div class="">sel tthel</div><div class=""><br class=""></div><div class="">(B) If you wanted to identify 3-10 helices directly from the structure (say it was just a model you built or some other undeposited structure), you could use the FindHBond tool or command and then identify where the mainchain H-bonds are i,i+3, and whether the conformation appears helical. I don’t think it is obvious from the backbone angles whether it is alpha or 3-10 helix. For example with 3kk4</div><div class=""><br class=""></div><div class="">select helix & @n,o</div><div class="">hbonds selRestrict both log true</div><div class=""><br class=""></div><div class="">…and then look in the Reply Log for i,i+3 backbone H-bonds. For chain A I get:</div><div class=""><br class=""></div><div class=""><div class="">H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):</div><div class="">GLU 3.A N ASN -1.A O no hydrogen 2.948 N/A</div><div class="">ILE 4.A N ALA 0.A O no hydrogen 2.993 N/A</div><div class="">PHE 5.A N MSE 1.A O no hydrogen 3.085 N/A</div><div class="">ILE 6.A N CME 2.A O no hydrogen 2.832 N/A</div><div class="">SER 12.A N ASN 9.A O no hydrogen 2.979 N/A</div><div class="">TYR 13.A N GLN 10.A O no hydrogen 3.327 N/A</div><div class="">LEU 34.A N SER 12.A O no hydrogen 2.914 N/A</div><div class="">ASP 37.A N GLN 33.A O no hydrogen 2.912 N/A</div><div class="">VAL 38.A N LEU 34.A O no hydrogen 2.904 N/A</div><div class="">[…]</div><div class="">GLU 88.A N VAL 84.A O no hydrogen 2.885 N/A</div><div class="">SER 101.A N PRO 98.A O no hydrogen 3.050 N/A</div><div class="">LEU 102.A N ILE 99.A O no hydrogen 2.968 N/A</div><div class="">VAL 107.A N ASP 103.A O no hydrogen 2.991 N/A</div><div class="">LEU 108.A N ALA 104.A O no hydrogen 3.010 N/A</div><div class="">ARG 109.A N GLN 105.A O no hydrogen 3.055 N/A</div><div class="">LEU 115.A N PRO 112.A O no hydrogen 3.035 N/A</div></div><div class="">53 hydrogen bonds found</div><div class=""><br class=""></div><div class="">… whereas if I just select the residues that the PDB file says are 3-10 </div><div class=""><br class=""></div><div class="">select tthel & @n,o</div><div class="">hbonds selRes both log t</div><div class=""><br class=""></div><div class="">I get:</div><div class=""><div class="">H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):</div><div class="">SER 12.A N ASN 9.A O no hydrogen 2.979 N/A</div><div class="">SER 12.A N ASN 9.A OD1 no hydrogen 3.067 N/A</div><div class="">SER 12.A OG ASN 9.A O no hydrogen 2.589 N/A</div><div class="">TYR 13.A N GLN 10.A O no hydrogen 3.327 N/A</div><div class="">SER 101.A N PRO 98.A O no hydrogen 3.050 N/A</div><div class="">LEU 102.A N ILE 99.A O no hydrogen 2.968 N/A</div><div class="">LEU 115.A N PRO 112.A O no hydrogen 3.035 N/A</div><div class="">7 hydrogen bonds found</div></div><div class=""><br class=""></div><div class="">(C) I don’t think you can tell 3-10 from other helix using just phi-psi angles, but to examine those angles you can show the protein Ramachandran Plot (Favorites… Model Panel, choose model on the left and then the Ramachandran plot button on the right). Then when you select any residue(s) they will show up on the plot as red dots. </div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html</a>></div><div class="">Or, you can select any single residue and click the green magnifying glass on the lower right corner of the Chimera window to show the Selection Inspector, then in that dialog choose to Inspect: “Residue” and it shows you the phi angle and psi angle values.</div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine</div><div class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D.<br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""></div><br class=""><blockquote type="cite" class="">On Oct 15, 2018, at 11:47 AM, BuddySphinx <<a href="mailto:yangqi.gu@yale.edu" class="">yangqi.gu@yale.edu</a>> wrote:<br class=""><br class="">Dear Chimera users,<br class="">I am wondering if there is a quick way in Chimera to visualize 3-10 helix? Or showing the dihedral angle of the peptide bonds?<br class="">Best,<br class="">Yangqi<br class=""></blockquote><br class=""></div></body></html>