<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 Hernando,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Perhaps runCommand should return a value but it doesn’t. The reasoning there was that the argument to runCommand could be anything, including several commands separated by semi-colons, so in some cases it’s confusing what the return value should be. In any case that ship has sailed and you have to do something else to get the value. In most cases it calling the underlying function that performs the command and using it’s return value, but looking at the code that implements the “measure center” command I can see that it doesn’t return anything either.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>So in the particular case of the example you provided, I can see two options for getting the value:</div><div class=""><br class=""></div><div class="">Option 1)</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>atoms = chimera.selection.OSLSelection(“#0:.A@CA”).vertices()</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>center = chimera.Point([a.coord() for a in atoms])</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>x, y, z = center.data()</div><div class=""><br class=""></div><div class="">Option 2)</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>rc(“sel #0:.A@CA”)</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>center = chimera.Point([a.coord() for a in chimera.selection.currentAtoms()])</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>x, y, z = center.data()</div><div class=""><br class=""></div><div class="">I hope this helps.</div><div class=""><br class=""></div><div class="">—Eric</div><div 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>
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<div><br class=""><blockquote type="cite" class=""><div class="">On Jun 8, 2018, at 11:10 AM, Hernando J Sosa <<a href="mailto:hernando.sosa@einstein.yu.edu" class="">hernando.sosa@einstein.yu.edu</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: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Dear Chimera,<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Is it possible to assign the result of running a chimera command in python to a string or something else? E.g doing something like:<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">from chimera import runCommand as rc<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">myresult = rc('measure center #0:.A@CA')<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">And then using the myresults somewhere else in the script after parsing for the relevant values?<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Maybe there is a n easier way to accomplish this?<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hernando<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></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; 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