<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi David,<DIV>I forgot to mention that swapaa and SCWRL do not move the backbone. Further modeling approaches would be needed if you intend to examine conformational changes in the backbone.<DIV>Elaine</DIV><DIV><BR><DIV><DIV>On Nov 22, 2006, at 2:34 PM, Elaine Meng wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Hi David,<DIV>The swapaa command needs the 3-letter residue name, for example</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>swapaa pro #0:24</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>It should be noted, however, that swapaa is a fairly crude way of looking at mutations. It will not adjust the positions of atoms in other residues, and the coordinates of the one you just "swapped" are not necessarily reasonable. Situations where I would use "swapaa" are when I plan to rotate the sidechain of the new residue myself.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>In the future, we plan to have Chimera know about reasonable conformations of amino acid side chains (rotamers) and possibly try to use a conformation that does not clash with the other atoms. For now, you can look at clashes with the Find Contacts/Clashes tool (under Tools... Structure Analysis).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Apart from Chimera, you might want to take a look at the program SCWRL. I believe it is free for noncommercial use from the Dunbrack group:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><A href="http://dunbrack.fccc.edu/SCWRL3.php">http://dunbrack.fccc.edu/SCWRL3.php</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>SCWRL isn't graphical, but you could view the output in Chimera.</DIV><DIV>Elaine</DIV><DIV><BR><DIV><DIV>On Nov 22, 2006, at 10:57 AM, Ng, David ((NIH/NCI)) [E] wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <DIV class="Section1"><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Hi,<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I’m currently learning to use Chimera. I wish to look at specific amino acid mutations in CDKN2A for effects in conformational changes and changes in protein interactions with known partners.<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">When I type the command “swapaa P #0:24” in chimera to mutate arginine 24 to proline in CDKN2A, I get an error message that says “Value error: No connectivity template for residue P” <O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Can you help me with this issue? Thanks.<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">David Ng, M.D.<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Staff Clinician</SPAN></FONT><O:P></O:P></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P> </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> <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; "><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><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></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> <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; "><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><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></DIV></BODY></HTML>