<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="">Elaine’s response caused me to realize the other problem with your script — you are going to need to add “; wait” to the end of any rock/roll/turn command you use. Otherwise the script will keep going without any frames being drawn, which also means that no motion from the rock/roll/turn will have occurred, and therefore the coordinates will be unchanged when the script reaches your “write” command.<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>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Dec 1, 2016, at 1:04 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Michael,<br class="">I was unable to reproduce this problem… I tried “turn y 90” and then "write #0 ~/Desktop/test.pdb” and it did write the transformed coordinates, and should behave the same way if run via python with rc. I guess you can doublecheck by actually typing commands (let us know if still problematic) and then make sure the same commands are used in your script.<br class=""><br class="">A separate issue: I see your script uses “rock” whereas you probably wanted “roll” or “turn” … note that “rock y 10 1” will not rotate 10 degrees, but perform 1 frame of a rocking oscillation that would have covered a 10 X 20 = 200-degree angle had it been allowed to perform a full cycle of 136 frames. Instead use “turn y 10” or “roll y 10 1” if you want to rotate 10 degrees around Y.<br class=""><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rock.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rock.html</a>><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br 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="">On Dec 1, 2016, at 10:23 AM, Michael Elbaum <<a href="mailto:michael.elbaum@weizmann.ac.il" class="">michael.elbaum@weizmann.ac.il</a>> wrote:<br class=""><br class=""><blockquote type="cite" class="">Dear Chimera people,<br class=""><br class="">I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates.<br class=""><br class="">I've tried the following:<br class="">for i in xrange(0,90,10):<br class=""> rc("rock " + "y " + str(i) + " 1")<br class=""> fn = basefn + str(i) + '.pdb'<br class=""> rc("write format pdb 0 " + fn)<br class="">and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11.<br class=""><br class="">thanks for your help,<br class="">Michael<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>