<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><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>Hi Tom,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I want to find out coordinates between peptide and protein. In x-ray structures (such as: 2gzv it is a PDZ domain and peptide binds to alpha helix in this domain), peptide is attached into C-terminal of protein. At least they obtained bound structure with attaching peptide into C-terminal of protein. Originally, peptide binds to different place in the protein. </DIV><DIV>Is there anyway to find the right place of peptide using this x-ray structure in Chimera? </DIV><DIV>If I find positions between peptide and protein, eventually i will see peptide-protein interactions as in the right place.</DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><DIV>I hope this clarifies my problem.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Nevin</DIV><BR><DIV><DIV>On Sep 27, 2007, at 3:05 PM, Thomas Goddard 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 Nevin,</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; "><SPAN class="Apple-converted-space"> </SPAN>Is your question about seeing a peptide in an x-ray density map?<SPAN class="Apple-converted-space"> </SPAN>Or is about contacts between peptide and protein atomic models (PDB files)?</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; ">> Is there any way to reconstruct x-ray structure data with the right</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">> peptide binding information?</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 don't understand this question.<SPAN class="Apple-converted-space"> </SPAN>Can you provide more details.</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; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>Tom</DIV> </BLOCKQUOTE></DIV><BR></BODY></HTML>