<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 Nancy,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The script assumes you only have one model open and flips that model in its entirety. Here’s a slightly tweaked version that flips all open molecular models:</div><div class=""><br class=""></div><div class="">from chimera import openModels, Molecule</div><div class="">for m in openModels.list(modelTypes=[Molecule]):</div><div class=""><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for a in m.atoms:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>crd = a.coord()</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>crd.x = 0 - crd.x</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>a.setCoord(crd)</div><div class=""><br class=""></div><div class="">You don’t <i class="">have</i> to type it into the IDLE shell. Instead, you could save the above into a file whose name ends in ‘.py’ (indicating it’s a Python file). The you could run the script simply by opening it in Chimera with File→Open or the “open” command.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I don’t know what you read on GitHub, but if you really need to restrict the script to working on a model with a particular ID#, it’s possible to make the script do that. Let me know if that’s what you need.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>It would be weird to flip just part of a model. Consider a model with two chains where the Z coordinate of all the atoms are in the range 30-40. Flipping the Z coordinate of one of the chains would move it far away from the other chain.</div><div class=""><br class=""></div><div class="">—Eric</div><br class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">On Sep 1, 2018, at 8:32 AM, Chu Ji <<a href="mailto:nancyji0217@gmail.com" class="">nancyji0217@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; 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 style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Eric,</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I was trying to get a mirror image of a PDB model and came across your thread. I know that you are typing in<span class="Apple-converted-space"> </span></div><div class=""><pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; background-color: rgb(246, 248, 250); background-position: initial initial; background-repeat: initial initial;" class=""><code style="font-family: "Courier New";" class=""><span style="font-family: Consolas; color: rgb(36, 41, 46); border: 1pt none windowtext; padding: 0in;" class="">m = chimera.openModels.list()[0]<o:p class=""></o:p></span></code></pre><pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; background-color: rgb(246, 248, 250); background-position: initial initial; background-repeat: initial initial;" class=""><code style="font-family: "Courier New";" class=""><span style="font-family: Consolas; color: rgb(36, 41, 46); border: 1pt none windowtext; padding: 0in;" class="">for a in m.atoms:<o:p class=""></o:p></span></code></pre><pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; background-color: rgb(246, 248, 250); background-position: initial initial; background-repeat: initial initial;" class=""><code style="font-family: "Courier New";" class=""><span style="font-family: Consolas; color: rgb(36, 41, 46); border: 1pt none windowtext; padding: 0in;" class=""> crd = a.coord()<o:p class=""></o:p></span></code></pre><pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; background-color: rgb(246, 248, 250); background-position: initial initial; background-repeat: initial initial;" class=""><code style="font-family: "Courier New";" class=""><span style="font-family: Consolas; color: rgb(36, 41, 46); border: 1pt none windowtext; padding: 0in;" class=""> crd.z = 0 - crd.z<o:p class=""></o:p></span></code></pre><pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; background-color: rgb(246, 248, 250); background-position: initial initial; background-repeat: initial initial;" class=""><code style="font-family: "Courier New";" class=""><span style="font-family: Consolas; color: rgb(36, 41, 46); border: 1pt none windowtext; padding: 0in;" class=""> a.setCoord(crd)</span></code><span style="font-family: Consolas; color: rgb(36, 41, 46);" class=""><o:p class=""></o:p></span></pre></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">in the Gen Control>IDLE section, but I also read on GitHub that I should<span class="Apple-converted-space"> </span><b class="">change the [0] in<span class="Apple-converted-space"> </span></b><code style="font-family: "Courier New";" class=""><b class=""><span style="font-size: 10pt; font-family: Consolas; color: rgb(36, 41, 46); border: 1pt none windowtext; padding: 0in;" class="">openModels.list()[0]</span></b></code><code style="font-family: "Courier New";" class=""><span style="font-size: 10pt; font-family: Consolas; color: rgb(36, 41, 46); border: 1pt none windowtext; padding: 0in;" class="">to the model specifier. What does that mean exactly? I tried to type in the PDB ID to replace the 0 but nothing happened…Could you show me an example? What if I want to flip Chain B of a certain model or just the entire model?<o:p class=""></o:p></span></code></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thank you so much for your help! Looking forward to hearing from you.</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best,</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Nancy</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Sent from<span class="Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">Mail</a><span class="Apple-converted-space"> </span>for Windows 10</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></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: 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; 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: 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;" class=""><span 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; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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="">Chimera-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: 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;" class=""><span 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; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>