<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style>
</head>
<body ocsi="0" fpstyle="1" class="" style="word-wrap:break-word">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Thanks Elaine and Erik! I changed to turn but the wait step was the key. It seems the writing got out of sync with the transform otherwise. working now :-)<br>
regards,<br>
Michael<br>
<br>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF920973"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Eric Pettersen [pett@cgl.ucsf.edu]<br>
<b>Sent:</b> Thursday, December 01, 2016 23:12<br>
<b>To:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Cc:</b> Michael Elbaum<br>
<b>Subject:</b> Re: [Chimera-users] saving pdb with transformed coordinates<br>
</font><br>
</div>
<div></div>
<div>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 class="" 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; word-wrap:break-word">
<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>
</div>
<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="" target="_blank">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="" target="_blank">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="" target="_blank">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="" target="_blank">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="" target="_blank">
Chimera-users@cgl.ucsf.edu</a><br class="">
Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="" target="_blank">
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class="">
<br class="">
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</div>
</body>
</html>