<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Turns out the "shape triangle" command is only in the Chimera daily build, not the current production version. The daily build is available on the Chimera download page and is usually as reliable as the production version.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 8, 2016, at 6:20 PM, Henrique C. S. Junior wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family:monospace,monospace"><div class="gmail_default" style="font-size:12.8px">That is weird, I'm receiving the message "Unknown shape: triangle" but the command line does recognize shape tube and etc.</div><div class="gmail_default" style="font-size:12.8px">I'm on Chimera 1.10.2 (b 40686) - Win 32.</div></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2016-03-08 14:47 GMT-03:00 Henrique C. S. Junior :<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class="gmail_default" style="font-family:monospace,monospace">Dear Elaine, thank you for your kind reply, your answers are always very complete.</div><div class="gmail_default" style="font-family:monospace,monospace">I'll give it a try ASAP.</div></div><div class="gmail_extra"><div class=""><div class="h5"><br class=""><div class="gmail_quote">2016-03-08 14:28 GMT-03:00 Elaine Meng :<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Dear Henrique,<div class="">You can use the “shape triangle” command to draw a triangle with three specified atoms at the points. You’d open the structure and then specify the 3 atoms (either by name and residue number, or by selection) in the command.</div><div class=""><br class=""></div><div class="">For example, commands:</div><div class=""><br class=""></div><div class="">open 4ysa</div><div class="">shape triangle atoms :401.A@CU:143.A@ND1:148.A@SD color sky blue</div><div class=""><br class=""></div><div class="">Or it may be easier for you to use selection instead of giving the residue numbers and atom names. Just Ctrl-click the first atom and then Shift-Ctrl-click the second and third atoms. When you have the three atoms you want selected, you could use this simpler command:</div><div class=""><br class=""></div><div class="">shape triangle atoms sel color orange</div><div class="">~select</div><div class=""><br class=""></div><div class="">… where ~select just clears (deselects) the selection. Details of “shape triangle”:</div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#triangle" target="_blank" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#triangle</a>></div><div class=""><br class=""></div><div class="">Example image attached below. The triangles are created as new models listed in the Model Panel, and you can hide or close them. Maybe it would work to make two triangles for your Cu2O2 case.</div><div class=""><br class=""></div><div class="">A completely different way would be to create a BILD format text file with “.polygon” descriptions of triangles and reading it in to Chimera. However, that is usually more bother since it requires creating a separate file. BILD format:</div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html" target="_blank" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">----------<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><span id="cid:3451485B-DC20-4C4E-A0FA-32B8B21A7816@compbio.ucsf.edu"><image.png></span></div><span class=""><br class=""><blockquote type="cite" class="">On Mar 8, 2016, at 5:23 AM, Henrique C. S. Junior wrote:<br class=""><br class="">Dear Chimera list,<br class="">As a inorganic chemist sometimes I have to deal with a variety of bridges (see image attached for an example) and it'd be very useful and didactic if I could create a little plane (like a distorted square) inside this bridges to mark different properties.<br class="">Is this possible in Chimera?<br class=""><br class="">Thank you in advance.<br class=""></blockquote><br class=""></span></div></div></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div></div></div><span class="">-- <br class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><span style="color:rgb(139,139,139)" class=""><font face="monospace, monospace" class=""><b class=""><font color="#808080" class="">Henrique C. S. Junior</font></b><br class="">Químico Industrial - UFRRJ</font></span></div><div dir="ltr" class=""><span style="color:rgb(139,139,139)" class=""><font face="monospace, monospace" class="">Mestrando em Química Inorgânica - UFRRJ<br class="">Centro de Processamento de Dados - PMP</font><br class=""></span></div></div></div></div></div></div>
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</blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><span style="color:rgb(139,139,139)" class=""><font face="monospace, monospace" class=""><b class=""><font color="#808080" class="">Henrique C. S. Junior</font></b><br class="">Químico Industrial - UFRRJ</font></span></div><div dir="ltr" class=""><span style="color:rgb(139,139,139)" class=""><font face="monospace, monospace" class="">Mestrando em Química Inorgânica - UFRRJ<br class="">Centro de Processamento de Dados - PMP</font><br class=""></span></div></div></div></div></div></div>
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