<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Dec 18, 2008, at 2:28 PM, Huang, Shengyou wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: -webkit-monospace; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; ">Is any way for Viewdock in Chimera to open a pdb file with NMR-style structures so that I can view those NMR-style structures one by one?</span></blockquote><br></div><div>Yes, you can use ViewDock for that. When ViewDock asks you what the file type is, choose either "Dock 3 or 3.5", "Dock 3.5.x single", or "Dock 4, 5 or 6". Then the normal ViewDock interface will come up. There won't be much information in the various fields because an NMR PDB file doesn't have the embedded information that a DOCK output file does, but nonetheless you can click through the list of structures like normal.</div><div><br></div><div>Another possibility is to open the NMR file as a trajectory (MD/Ensemble Analysis->MD Movie) and play through the conformations that way. You could also use other analysis capabilities of the MD Movie tool, such as the RMSD map function.</div><div><br></div><div>You might also want to try out the Ensemble Cluster tool, which will cluster your NMR ensemble and let you look at representative structures from each cluster.</div><div><br></div><div>It sounds like you have a lot of conformations, so the Ensemble Match (compare your N structures in an NxN table) and Tile Structures (show all the conformations at once tiled in a grid on the screen) are probably not as useful as they would be for smaller ensembles.</div><div><br></div><div>--Eric</div><div><div><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; "><br class="Apple-interchange-newline"> 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></div></div><br><div></div></div></body></html>