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<div>Hello <span style="color: rgb(49, 53, 59); font-family: Verdana, 'Microsoft Yahei', SimSun, sans-serif; line-height: 22.4px;">Eric,</span></div><div>Thank you so much for your help! It helps me a lot. I'm really appreciate that.</div><div> Leo</div>
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<a class="mail-from" style="color: #3061f2; text-decoration: none" href="mailto:pett@cgl.ucsf.edu">Eric Pettersen<pett@cgl.ucsf.edu>
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3/29/2023 23:54
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Re: [chimerax-users] measure distance to ring centroid
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<div id="ntes-pcmail-quote" style="margin: 0; padding: 0; font-size: 14px; font-family: '微软雅黑';">Hi Leo,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Yes, that's a bug. The bug has been fixed, but the fix is only in the daily build and 1.6 release candidate builds, so you would have to install one of those to get this to work. Sorry about that.</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 class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 29, 2023, at 6:19 AM, 12119007 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=""><meta charset="UTF-8" class=""><div style="caret-color: rgb(0, 0, 0); font-style: normal; font-variant-caps: normal; font-weight: 400; 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: 微软雅黑, Verdana, "Microsoft Yahei", SimSun, sans-serif; font-size: 14px; line-height: 1.6;" class=""><div class=""></div><div class=""><div class="">Hello Elaine,</div><div style="text-indent: 2em;" class="">Thank you so mach for your kindly help. I have succeeded in defining the centroids, but when I click the distance between centroids to the atom I chosed, it report this bug. I don't know if there's some thing I did wrong. Let me know if something I can do.Thank you so much.</div><div style="text-indent: 2em;" class=""> Leo </div><div style="text-indent: 2em;" class=""> </div><div class=""><span id="cid:B9BF7215-1488-4FCC-A517-BB4861A36F8D@mailmaster"><E473B256-5FCC-4823-AEEB-13A542E873EA.png></span><span class=""><span class="Apple-converted-space"> </span><br class=""></span></div><div class=""><span id="cid:64C196A8-5C8A-4232-977A-506DEEA955E6@mailmaster"><A52D4FCF-E872-44AE-A88F-BD86DC514908.png></span><span class=""><br class=""></span></div><div style="font-family: 微软雅黑;" class=""><div style="font-size: 14px; padding: 0px; margin: 0px; line-height: 14px;" class=""><div style="padding-bottom: 6px; margin-bottom: 10px; display: inline-block;" class=""><a href="https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=12119007&uid=12119007%40zju.edu.cn&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%2212119007%40zju.edu.cn%22%5D&logoUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyeicon%2Fdb5d090b4290fa1cc857f03f01662859.png" style="display: block; background-color: rgb(255, 255, 255); max-width: 400px; padding: 15px 0px 10px; text-decoration: none; outline: none;" class=""><table cellpadding="0" style="width: 400px; max-width: 100%; table-layout: fixed; border-collapse: collapse; color: rgb(155, 158, 161); font-size: 14px; line-height: 1.3;" class=""><tbody style="word-wrap: break-word; word-break: break-all; font-family: "PingFang SC", "Hiragino Sans GB", "WenQuanYi Micro Hei", "Microsoft Yahei", 微软雅黑, verdana !important;" class=""><tr class="firstRow"><td width="38" style="padding: 0px; box-sizing: border-box; width: 38px; word-break: break-all;"><img width="38" height="38" src="https://mail-online.nosdn.127.net/qiyelogo/defaultAvatar.png" style="vertical-align: middle; width: 38px; height: 38px; border-radius: 50%;" class=""></td><td style="padding: 0px 30px 0px 10px; color: rgb(49, 53, 59);"><div style="font-size: 16px; font-weight: bold; width: 250px; white-space: nowrap; overflow: hidden; text-overflow: ellipsis;" class="">12119007</div></td><td width="72" style="text-align: right; width: 72px;"><img width="72" height="20" src="https://mail-online.nosdn.127.net/qiyelogo/db5d090b4290fa1cc857f03f01662859.png" style="width: 72px; height: 20px;" class=""></td></tr><tr width="100%" style="width: 400px; font-size: 14px !important;" class=""><td colspan="3" style="padding: 10px 0px 0px; width: 400px; font-size: 14px !important;"><div style="width: 400px; word-wrap: break-word; word-break: break-all; font-size: 14px !important;" class="">12119007@zju.edu.cn</div></td></tr></tbody></table></a></div></div></div></div><div class="J-reply ntes-mailmaster-quote" style="padding-top: 1px; padding-bottom: 1px;"><div style="margin-top: 2em; margin-bottom: 1em; font-size: 14px; line-height: 1.25; color: rgb(120, 120, 122);" class="">---- Replied Message ----</div><div style="margin-bottom: 1em; font-size: 12px; line-height: 1.25; color: rgb(35, 35, 36); padding: 0.5em 0.25em; border-radius: 0.67em; background-color: rgb(240, 240, 240);" class=""><table width="100%" cellpadding="0" cellspacing="9" border="0" class=""><tbody class=""><tr class="firstRow"><td valign="top" style="width: 4.25em; font-size: 12px; line-height: 1.25; color: rgb(120, 120, 122);">From<span class="Apple-converted-space"> </span></td><td valign="top" style="font-size: 12px; line-height: 1.25; color: rgb(35, 35, 36); word-break: break-all;"><a class="mail-from" href="mailto:meng@cgl.ucsf.edu" style="color: rgb(48, 97, 242); text-decoration: none;">Elaine Meng<meng@cgl.ucsf.edu></a></td></tr><tr class=""><td valign="top" style="width: 4.25em; font-size: 12px; line-height: 1.25; color: rgb(120, 120, 122);">Date<span class="Apple-converted-space"> </span></td><td class="mail-date" valign="top" style="font-size: 12px; line-height: 1.25; color: rgb(35, 35, 36); word-break: break-all;">3/28/2023 23:45</td></tr><tr class=""><td valign="top" style="width: 4.25em; font-size: 12px; line-height: 1.25; color: rgb(120, 120, 122);">To<span class="Apple-converted-space"> </span></td><td valign="top" style="font-size: 12px; line-height: 1.25; color: rgb(35, 35, 36); word-break: break-all;"><a class="mail-to" href="mailto:12119007@zju.edu.cn" style="color: rgb(48, 97, 242); text-decoration: none;">12119007<12119007@zju.edu.cn></a></td></tr><tr class=""><td valign="top" style="width: 4.25em; font-size: 12px; line-height: 1.25; color: rgb(120, 120, 122);">Cc<span class="Apple-converted-space"> </span></td><td valign="top" style="font-size: 12px; line-height: 1.25; color: rgb(35, 35, 36); word-break: break-all;"><a class="mail-cc" href="mailto:chimerax-users@cgl.ucsf.edu" style="color: rgb(48, 97, 242); text-decoration: none;">Elaine Meng via ChimeraX-users<chimerax-users@cgl.ucsf.edu></a></td></tr><tr class=""><td valign="top" style="width: 4.25em; font-size: 12px; line-height: 1.25; color: rgb(120, 120, 122);">Subject<span class="Apple-converted-space"> </span></td><td class="mail-subject" valign="top" style="font-size: 12px; line-height: 1.25; color: rgb(35, 35, 36); word-break: break-all;">Re: [chimerax-users] measure distance to ring centroid</td></tr></tbody></table></div><div id="ntes-pcmail-quote" style="margin: 0px; padding: 0px; font-size: 14px; font-family: 微软雅黑;" class="">Small correction, the first link should be:<br class=""><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html</a>><br class=""><br class="">...or you can use ChimeraX command "help define" to show the same help page included with your download.<br class=""><br class=""><blockquote class="mmbqc1">On Mar 28, 2023, at 8:31 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hi Leo,<br class="">Your chimeraX image with yellow dashed line is showing the closest distance to the plane, which is not necessarily the center of the ring. To show a dashed line to the center of the ring you would need to calculate a centroid of the ring (instead of the plane of the ring) and then measure distance between the centroid and the atom.<br class=""><br class="">E.g. if you select the 6 ring atoms (Ctrl-click first atom, Shift-Ctrl-click each of the other 5) then you could use the Axes/Planes/Centroids tool or the "define" command to define their centroid, for example:<br class=""><br class="">define centroid sel radius 0.25<br class=""><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.htm" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.htm</a>><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html</a>><br class=""><br class="">Then you can measure distance between the centroid and the atom, e.g. Ctrl-click the centroid, Ctrl-Shift-doubleclick the atom and choose Distance from the resulting pop-up menu.<br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><blockquote class="mmbqc2">On Mar 28, 2023, at 3:52 AM, 12119007 via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hello chimerax developers pannel,<span class="Apple-converted-space"> </span><br class="">Bother to ask, I'm using chimerax to show an arginine forming a Π-cation bond with a phenyl ring， I don't know how to show the center of the phenyl ring like in pymol. I'm writing the order like this: distance /A:103@NH2 #1.4 and #1.4 is a plane I defined the phenyl ring. but it just show the distance but can't show the dash. Please tell me how to do. Any help I'm really appreciate. Thanks.<br class=""><BE054F93-9BD3-4FDC-9E49-660D67BD8069.png><E2104D7E-B06A-41FA-A3B2-3CAFE1FFD3D5.png> Leo<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""><br class=""></blockquote></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; float: none; display: inline !important;" class="">Manage subscription:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;" class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></div>
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