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Hi Randy,<div><span class="Apple-tab-span" style="white-space:pre"> </span>The disconnected hydrogens (H1, H2, H6) look like they should be bonded to the CA in residue 0. The problem is that the hydrogens are in residue 1 and Chimera will never form cross-residue bonds that involve hydrogen unless there are explicit connect records. Your options to fix this are:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>1) add CONECT records</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>2) put those hydrogens in residue 0 and reorder the PDB file</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>3) put all the atoms in residue 1 and give the CAs unique names. I recommend changing the residue name to something other than ALA in this case.</div><div><br></div><div>As a footnote for option 3, you don't actually _have_ to give the CAs unique names. You could still distinguish them in commands by serial number, e.g. color red @/serialNumber=1. It's just a whole lot easier to give them unique names. :-)</div><div><br></div><div>--Eric</div><div><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></span> </div><br><div><div>On May 27, 2008, at 10:56 AM, Randy Heiland wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I have a naive question - given the following pdb file:</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; ">ATOM<span class="Apple-converted-space"> </span>1<span class="Apple-converted-space"> </span>CA<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>0 <span class="Apple-converted-space"> </span>1.125 <span class="Apple-converted-space"> </span>1.534 <span class="Apple-converted-space"> </span>0.000<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>C</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>2<span class="Apple-converted-space"> </span>C <span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>0 <span class="Apple-converted-space"> </span>0.000 <span class="Apple-converted-space"> </span>0.514 <span class="Apple-converted-space"> </span>0.000<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>C</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>3<span class="Apple-converted-space"> </span>O <span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>-1.173 <span class="Apple-converted-space"> </span>0.853 <span class="Apple-converted-space"> </span>0.000<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>O</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>4<span class="Apple-converted-space"> </span>N <span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1 <span class="Apple-converted-space"> </span>0.394<span class="Apple-converted-space"> </span>-0.796 <span class="Apple-converted-space"> </span>0.000<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>N</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>5<span class="Apple-converted-space"> </span>CA<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1<span class="Apple-converted-space"> </span>-0.546<span class="Apple-converted-space"> </span>-1.905 <span class="Apple-converted-space"> </span>0.000<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>C</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>6<span class="Apple-converted-space"> </span>H1<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1 <span class="Apple-converted-space"> </span>1.017 <span class="Apple-converted-space"> </span>2.171 <span class="Apple-converted-space"> </span>0.880<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>H</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>7<span class="Apple-converted-space"> </span>H2<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1 <span class="Apple-converted-space"> </span>1.017 <span class="Apple-converted-space"> </span>2.171<span class="Apple-converted-space"> </span>-0.880<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>H</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>8<span class="Apple-converted-space"> </span>H3<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1 <span class="Apple-converted-space"> </span>1.381<span class="Apple-converted-space"> </span>-0.999 <span class="Apple-converted-space"> </span>0.000<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>H</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>9<span class="Apple-converted-space"> </span>H4<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1<span class="Apple-converted-space"> </span>-1.551<span class="Apple-converted-space"> </span>-1.486 <span class="Apple-converted-space"> </span>0.000<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>H</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <span class="Apple-converted-space"> </span>10<span class="Apple-converted-space"> </span>H5<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1<span class="Apple-converted-space"> </span>-0.420<span class="Apple-converted-space"> </span>-2.528<span class="Apple-converted-space"> </span>-0.890<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>H</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <span class="Apple-converted-space"> </span>11<span class="Apple-converted-space"> </span>H6<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1 <span class="Apple-converted-space"> </span>2.123 <span class="Apple-converted-space"> </span>1.091 <span class="Apple-converted-space"> </span>0.000<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>H</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <span class="Apple-converted-space"> </span>12<span class="Apple-converted-space"> </span>H7<span class="Apple-converted-space"> </span>ALA <span class="Apple-converted-space"> </span>1<span class="Apple-converted-space"> </span>-0.420<span class="Apple-converted-space"> </span>-2.528 <span class="Apple-converted-space"> </span>0.890<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">0.00<span class="Apple-converted-space"> </span>0<span class="Apple-converted-space"> </span>H</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; ">when I display it in Chimera, there are 3 unbonded hydrogens - why is <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">that and is there a menu item to create/display the bonds?</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, Randy</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; ">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>