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Thank you Elaine and Tom. That was very useful although i seem to have some trouble encoding the movie. It throws up a Python error that could be a version problem. I shall update to the latest version and check again.
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<div class="">The other question i had was how do i fit a model onto the tomogram volume, specifically a 3D structure obtained from subtomogram averaging? Is this possible in the current latest version of chimera? Ideally i would like the planes of the tomogram
volume to move through one way and the 3D structure coming up as it moves up the other way.</div>
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<div class="">Thanks,</div>
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<div class="">Swetha</div>
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<div class=""><b class="">Dr Swetha Vijayakrishnan</b></div>
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<div class="" style="orphans: 2; widows: 2;"><b class="">MRC-University of Glasgow Centre for Virus Research (CVR)</b></div>
<div class="" style="orphans: 2; widows: 2;">University of Glasgow,</div>
<div class="" style="orphans: 2; widows: 2;">Sir Michael Stoker Building,</div>
<div class="" style="orphans: 2; widows: 2;">464 Bearsden Road, </div>
<div class="" style="orphans: 2; widows: 2;">Garscube campus </div>
<div class="" style="orphans: 2; widows: 2;">Glasgow G61 1QH</div>
<div class="" style="orphans: 2; widows: 2;">UK</div>
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<div class="">Email: <a href="mailto:Swetha.Vijayakrishnan@glasgow.ac.uk" class="">
Swetha.Vijayakrishnan@glasgow.ac.uk</a></div>
<div class="">Phone: +44 (0) 141 330 4025</div>
<div class=""> <a href="http://www.gla.ac.uk/colleges/mvls/supportforresearch/nerd/" class="">http://www.gla.ac.uk/colleges/mvls/supportforresearch/nerd/</a></div>
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<div class="">On 15 Sep 2017, at 18:35, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div>
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<div class="">In brief the command to play through volume planes 0-75 looks like<br class="">
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<span class="Apple-tab-span" style="white-space:pre"></span>volume #0 planes z,0,75<br class="">
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and to record a movie with that you could use<br class="">
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<span class="Apple-tab-span" style="white-space:pre"></span>movie record ; volume #0 planes z,0,75 ; wait 75 ; movie encode ~/Desktop/planes.mp4<br class="">
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Instead of typing in the command line you can put those commands in a file with suffix “.cmd” and open it, helpful when you add more commands.<br class="">
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<span class="Apple-tab-span" style="white-space:pre"></span>Tom<br class="">
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<blockquote type="cite" class="">On Sep 15, 2017, at 9:19 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
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Hi Sweta,<br class="">
If I understand correctly, you have one volume data set and want to play through its planes. (Volume Series is for when you have multiple 3D data sets.) It sounds like you are using the slider in the Planes section of Volume Viewer to do it manually. <br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes</a>><br class="">
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To do it automatically, as you would want for a movie script, you can use the “volume” command “planes” option:<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes</a>><br class="">
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There is a nice little example at the bottom of this page… you can click the image to see the short movie and then follow the link to see the script that was used:<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html" class="">http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html</a>><br class="">
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I hope this helps,<br class="">
Elaine<br class="">
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Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
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<blockquote type="cite" class="">On Sep 15, 2017, at 6:19 AM, Swetha Vijayakrishnan <<a href="mailto:Swetha.Vijayakrishnan@glasgow.ac.uk" class="">Swetha.Vijayakrishnan@glasgow.ac.uk</a>> wrote:<br class="">
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Dear All,<br class="">
I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie.
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I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the
right way to do it?<br class="">
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Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated.<br class="">
Thanks and best wishes,<br class="">
Swetha <br class="">
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