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Hi James,<div>There are many different secondary structure assignment methods (and sets of parameters), and they often disagree to various extents. If the PDB file has HELIX and SHEET information in it, that will be used. Take a look in the files - if they do have such information, it comes from the depositor, and different depositors have used different methods.</div><div><br></div><div>If files do not have that information, Chimera will perform an assignment. Chimera uses "ksdssp" and there is no other choice of method, but you can adjust the parameters that it uses by default by choosing "compute SS" from the Model Panel, see:</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#computess">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#computess</a></font></div></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html</a></font></div></div><div><br></div><div>Also by default, MatchMaker runs "ksdssp" - it uses both sequence and secondary structure information to align structures, and we found it tends to improve the superpositions when a consistent secondary structure assignment method is used on all the structures being aligned. Nevertheless, you can turn off the option to run "ksdssp" beforehand. (Need to re-open the structure files to get back their original assignments, however.)</div><div><br></div><div>There is no real gold standard of what is a helix and what is a strand. There is no problem when the structure is nearly ideal, only as it becomes less regular or shorter. Thus it is hard to say something is definitely wrong. However, if to your eye you would prefer something to be assigned as a strand, you can just set it manually with Selection Inspector or "setattr" as described here:</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001775.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001775.html</a></font></div></div><div><br></div><div>To display both backbone atoms and ribbon, use the command "ribbackbone" - it may not look very good, however, as the ribbon is a smoothed interpolation... the atoms may not fall right on top of the ribbon in some places.</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html</a></font></div></div><div><br></div><div>Best,</div><div>Elaine</div><div><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><div><br></div><div><div><div>On May 2, 2008, at 2:19 PM, James Fethiere wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <font face="Helvetica, Arial, sans-serif">Hi,<br> I'm seing something strange with secondary structure assignments in peptides. Two examples: PDB 1axc has a peptide bound to PCNA with beta strand interactions and chimera doesn't pick it up as a strand. In the other example, 1rxz, it picks up the strand in a similar peptide but the strand disappear when I run matchmaker with 1ul1 (which also has a strand at the c-terminus that is not picked up. Is there any explanation? Are the criteria for secondary structure assignments to strict?<br> <br> One more thing that may have been asked already!! how does one keeps the NH and CO of the peptide bond displayed in the ribbons view?<br> Thanks<br> James<br> </font><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div></blockquote></div><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; "><br class="Apple-interchange-newline"></span> </div><br></div></body></html>