<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">This message and the one before it reappeared due to a malfunction in our mailing-list software. That problem has been fixed. Sorry for the spam. The problem in the mail itself has been fixed also, as per the response I sent to the original messages.<div><br></div><div>--Eric</div><div><br><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div></span></div><div><div>On Jul 16, 2010, at 2:58 AM, Gesa Volkers wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Eric,<br><br>thanks for your suggestions. Unfortunately removing the SEQRES record <br>did not help. I also downloaded and installed the new chimera-version <br>today. The false numbering in the alignment still occurs. Also when I <br>remove the SEQRES record and try with the new chimera version the false <br>numbering appears. Quite annoying... The pdb-file is not in the protein <br>data bank yet.<br><br>Any more suggestions? Could I add "dummy atoms" in the structure?<br><br>Thanks,<br>Gesa<br><br><br><br>Eric Pettersen schrieb:<br><blockquote type="cite">On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Dear All,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I observed an issue with the alignment function of Chimera.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I loaded a crystal structure where in between a loop is not modelled <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">due to low electron density- so these residues are missing in the <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">structure and the numbering also has this gap. When I align this <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">structure with others, the missing residues are not recognized and <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">chimera just overrides the numbering so after this loop all the <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">numbers in the alignment do not fit anymore to the residues they <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">should belong to although the structure and numberings are shown in <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the right way in the graphics window. How can I overcome this issue? <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Should I change the pdb-file? In which way?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks for all responses!<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi Gesa,<br></blockquote><blockquote type="cite">I had a similar problem reported with 1JFF 12 days ago and haven't yet <br></blockquote><blockquote type="cite">worked on fixing it. It seems to only happen for a small subset of <br></blockquote><blockquote type="cite">structures. 1JFF has a missing loop and also exactly one missing <br></blockquote><blockquote type="cite">residue at the N terminus. Is your structure like that? Is it a <br></blockquote><blockquote type="cite">standard PDB entry (if so, what's the ID code)? I'll add you to the <br></blockquote><blockquote type="cite">recipient list for the ticket we have open in our bug database for <br></blockquote><blockquote type="cite">this (#8585) so you will be notified when it gets fixed. It'll <br></blockquote><blockquote type="cite">probably be fairly soon.<br></blockquote><blockquote type="cite">Until then the only workaround that occurs to me is for you to remove <br></blockquote><blockquote type="cite">the SEQRES records from the PDB file before you open it. Then the <br></blockquote><blockquote type="cite">Sequence viewer will depict only the residues physically present in <br></blockquote><blockquote type="cite">the structure -- no gaps (incorrect or otherwise) will be depicted.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--Eric<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Eric Pettersen<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> UCSF Computer Graphics Lab<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br><br>-- <br>Gesa Volkers<br>Institut für Biochemie, Molekulare Strukturbiologie<br>Felix-Hausdorff-Straße 4<br>17489 Greifswald<br>Germany<br>+49 (3834)-864392<br><br><br>_______________________________________________<br>Chimera-dev mailing list<br><a href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev<br><br></div></blockquote></div><br></div><br></body></html>