<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Michael,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>A line of Python code was mis-indented, causing pairwise RMSDs in the alignment header to be too small by a factor of 1/<span style="caret-color: rgb(32, 33, 36); color: rgb(32, 33, 36); font-family: arial, sans-serif; font-size: 14px; background-color: rgb(255, 255, 255);" class="">√</span>2. It's too late for us to feel comfortable putting this fix/change in the 1.5 release (which is coming out tonight), but it will be in tomorrow's daily build. Thanks for alerting us to this.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 24, 2022, at 2:12 AM, Michael Habeck via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);">Dear ChimeraX forum,</div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="ContentPasted1 elementToProof ContentPasted0 ContentPasted4" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);">I'm interested in getting the distance between Cα for all residues in an alignment. I've noticed that the Cα RMSD values in the txt file obtained from the header of the sequence alignment created by matchmaker via </div><div class="elementToProof ContentPasted1 ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""><br class=""></span></div><div class="elementToProof ContentPasted1 ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class="">sequence header rmsd save </span><br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="ContentPasted2 elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);">are different from the distances measured using the rmsd or distance command. The <span class="ContentPasted3" style="background-color: rgb(255, 255, 255); display: inline !important;">Cα distance measured is approx. 41% higher across the entire alignment than in the saved output. When selecting a pair of aligned residues from the alignment viewer, the distance shown does not match the one in the output file but the distance measurement. I've attached a file with the respective distances for the alignment of chains A in 3c4f and 3gqi as an example. </span></div><div class="ContentPasted2 elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);"><span class="ContentPasted3" style="background-color: rgb(255, 255, 255); display: inline !important;"><br class=""></span></div><div class="ContentPasted2 elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);"><span class="ContentPasted3" style="background-color: rgb(255, 255, 255); display: inline !important;">Not sure if this is a misunderstanding from my side or a bug, yet I'd greatly appreciate a clarification of the differences.</span></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);">With thanks in advance and best regards,</div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; background-color: rgb(255, 255, 255);">Michael</div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div id="Signature" class=""><div name="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; margin: 0px;" class=""></div></div></div><span id="cid:2548B529-ADDA-45E0-A9A0-3B6CEDD468B9"><header_vs_distance_mm_3c4f-a_3gqi-4.txt></span><span style="caret-color: rgb(0, 0, 0); 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