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You can also make Chimera add D amino acids via a relatively simple change in its Python code. If you edit <your Chimera installation>/share/Rotamers/__init__.py, you will find a line that looks like this:<div><br></div><div> xform, rmsd = matchPositions(_coordArray([n, ca, c]),</div><div><br></div><div>(approximately line #53). Change it to this:</div><div><br></div><div> xform, rmsd = matchPositions(_coordArray([c, ca, n]),</div><div><br></div><div>i.e. swap the 'c' and then 'n'. This will have the effect of making it place the CB atom at the D position instead of the L position. Of course, when you are done make sure to swap the c and the n back or Chimera will add D amino acids forever. The other thing to keep in mind is that the rotamer libraries are developed for L amino acids and therefore are basically of little assistance in choosing a side chain conformation for D amino acids.</div><div><br></div><div>--Eric<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: 16px; 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; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span> </div><br><div><div>On Jun 30, 2008, at 10:53 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Yasser,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sorry, mutation with the Rotamers tool (or swapaa command) is only to <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">L-amino acids.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Some less convenient alternatives:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- use Build Structure (under Tools... Structure Editing) to build out <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the D- side chain manually.<span class="Apple-converted-space"> </span>Note the resulting bond lengths and <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">angles are approximate.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- open another structure that contains the D- amino acid, match the <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">backbone atoms of the residue you wish to substitute, write out <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">coordinates "relative to" the first structure, then manually edit the <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">PDB file to substitute that sidechain for the one originally in the <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">structure.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I hope this helps,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Elaine</div><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; ">Elaine C. Meng, Ph.D.<span class="Apple-converted-space"> </span><a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">UCSF Computer Graphics Lab and Babbitt Lab</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Department of Pharmaceutical Chemistry</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of California, San Francisco</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Jun 27, 2008, at 12:33 PM, Yasser Almeida Hernández wrote:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can Chimera mutate by D-residues? If this is possible, how i can do <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">it?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks...</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Yasser Almeida Hernández</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Estudiante, 4to Año Bioquímica</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Facultad de Biología</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Universidad de la Habana</div> </blockquote><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></body></html>