<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div><span>Elaine:</span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: HelveticaNeue-Light, 'Helvetica Neue Light', 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: HelveticaNeue-Light, 'Helvetica Neue Light', 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><span>Thanks so much! I will give it try. Regards, Jesse</span></div> <div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: HelveticaNeue-Light, 'Helvetica Neue Light', 'Helvetica Neue',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 16px;"> <div dir="ltr"> <font size="2" face="Arial"> On Monday, October 6, 2014 5:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:<br> </font> </div> <br><br> <div class="y_msg_container">Hi Jesse,<br clear="none">We're glad you like Chimera, and are always happy to hear about classroom use!<br clear="none"><br clear="none">As you probably saw, "Build Structure" doesn't have an option for D-amino acids. However, you can use it to build the L-amino acid version of the peptide, then invert the chirality of each residue. In a little more detail:<br clear="none"><br clear="none">(1) start Build Structure (in menu under Tools… Structure Editing)<br clear="none"><br clear="none">(2) in that tool, use the "Start Structure" section to create the L-amino acid
version of your peptide sequence: enter the sequence, Apply, then in the next dialog set the phi/psi angles<br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start</a>><br clear="none"><br clear="none">(3) invert the alpha-carbon of each residue, e.g. commands:<br clear="none"><br clear="none">invert :<a shape="rect" ymailto="mailto:1@ca" href="mailto:1@ca">1@ca</a><br clear="none">invert :<a shape="rect" ymailto="mailto:2@ca" href="mailto:2@ca">2@ca</a><br clear="none">(… etc. …)<br clear="none">invert :<a shape="rect" ymailto="mailto:10@ca" href="mailto:10@ca">10@ca</a><br clear="none"><br clear="none">Or, if you want to control exactly which two substituents on CA are swapped, you can name them in the command instead of the CA. If you wanted the H to
be one of the swapped substituents, you would have to add explicit hydrogens first. For example, commands:<br clear="none"><br clear="none">addh<br clear="none">invert :<a shape="rect" ymailto="mailto:1@ha" href="mailto:1@ha">1@ha</a>,cb<br clear="none">(etc.)<br clear="none"><br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html</a>><br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html</a>><br clear="none"><br clear="none">You can save the structure as a PDB file with menu: File… Save PDB, or command: write<br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb"
target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb</a>><br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html</a>><br clear="none"><br clear="none">I hope this helps,<br clear="none">Elaine<br clear="none">----------<br clear="none">Elaine C. Meng, Ph.D. <br clear="none">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br clear="none">Department of Pharmaceutical Chemistry<br clear="none">University of California, San Francisco<br clear="none"><br clear="none"><div class="yqt5507770437" id="yqtfd94694"><br clear="none">On Oct 6, 2014, at 10:52 AM, JESSE JAYNES <<a shape="rect" ymailto="mailto:jjsqrd@bellsouth.net" href="mailto:jjsqrd@bellsouth.net">jjsqrd@bellsouth.net</a>> wrote:<br clear="none"><br clear="none">> I am a long time user of Chimra and greatly
appreciate the software. I am also a professor at Tuskegee university and I use it in the classroom. I am Mac user.<br clear="none">> <br clear="none">> I have a question. <br clear="none">> <br clear="none">> How can I model an all D-form of a 10 amino acid peptide and generate its pdb?<br clear="none">> <br clear="none">> Thank you!<br clear="none">> <br clear="none">> Jesse M. Jaynes<br clear="none"></div><br><br></div> </div> </div> </div> </div></body></html>