<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jun 21, 2010, at 6:25 AM, S. Shunmugasundararaj wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Eric,<br><br>I am using Chimera v1.4. When aligning 2 or more structures, it gives the<br>RMSD as a bar graph. Is it possible to get the RMSD value for each residue?<br><br>Thanks<br>Raj</div></blockquote><br></div><div>Hi Raj,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I'm guessing the "RMSD as a bar graph" is the RMSD header at the top of the Multalign Viewer tool. You can save the header values to a file with the "Headers->Save..." menu entry at the top of the tool. This will save the RMSD value for each alignment position to a file. This may or may not be useful for you since the residues associated with each alignment position aren't indicated in the file.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Alternatively, each residue involved in the Multalign Viewer RMSD header calculation gets a "mavRMSD" attribute assigned to it. You can save these attributes to a file by using the "File->Save Attributes..." menu of the Render By Attribute tool (available in the Depiction and Structure Analysis tools menus).</div><div><br></div><div>--Eric</div><br><div apple-content-edited="true"> <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; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><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><br class="Apple-interchange-newline"></div></span> </div><br></body></html>