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<p><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 15px;">The viz package Amira has something similar called 'pack and go'. </span> And t<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 15px;">he video
editing software Final Cut Pro has 'media manager', which provides more control.</span></p>
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<p><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 15px;">It would be a useful option to bundle the whole working directory, including pdfs, spreadsheets, manuscript drafts. </span></p>
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<p>I also recommend in the design something that can include archival concepts, as opposed to only a comprehensive & reliable session transfer from person A to person B.</p>
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<p>When managing multiple session files over a period of years, it would be useful to get summaries of the blob of data; list of sizes, types, dates, etc., that can be examined without loading everything (which can take a long time if the files are big) just
to get a status. Having an archival snapshot button that generates jpegs that could be included would help sorting through large numbers of sessions, particularly if the person sorting them is not the person who created them. </p>
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<p>For example, Tom you helped me out on some python code that would do a backbone trace 6-15 years ago; if someone asked me to create another animation like that, it would be a fishing expedition in a terabyte sea. </p>
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<div class="PlainText">Matthew Dougherty<br>
National Center for Macromolecular Imaging<br>
Baylor College of Medicine<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Oliver Clarke <olibclarke@gmail.com><br>
<b>Sent:</b> Friday, September 11, 2015 3:04 PM<br>
<b>To:</b> Tom Goddard<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] Saving sessions including maps?</font>
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<div>Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!
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<div class="">One temporary work around I have thought about is the following alias:</div>
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<div class="">#Save session with maps. saves in home dir with directory name same as session.</div>
<div class=""># Usage: save_session_dir session-name</div>
<div class=""># Don't use spaces or under_scores in session names.</div>
<div class="">alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1</div>
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<div class="">This will save all maps in a subdir of the home directory with the desired session name, and then save the session in the same dir - this folder is then portable and has all the info needed to restore the session. The only caveat to this is that
this only works if the directory already exists - otherwise it gives an error. Maybe it would be possible to add an option to save/write to make the dir if it does not already exist? Otherwise I can do it in python I guess. Also, map names are not preserved,
but I don’t see any easy way to get around that. Only other problem with this is that because of the way aliases work in chimera, any underscores in the alias arguments will be converted to spaces, but that is not an issue so long as one is aware of it.</div>
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<div class="">Cheers,</div>
<div class="">Oliver.</div>
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<div class="">On Sep 11, 2015, at 6:54 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div>
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<div class="" style="word-wrap:break-word">Hi Oliver,
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<div class=""> This has long been a requested feature.</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span><a href="http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426" class="">http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426</a></div>
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<div class="">And I agree it would be useful. If Chimera packages up all the needed maps and the session file in a zip archive this would be convenient. You can of course do this right now by hand, only it isn’t so convenient. Unfortunately this has never
reached a high enough priority relative to other enhancements we are working on, so it has not been implemented. It is more likely to get into Chimera 2 than Chimera 1.</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div class="">On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:</div>
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<div class="">Hi all,<br class="">
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Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved?
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This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing.<br class="">
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It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain.<br class="">
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This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think?<br class="">
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Cheers,<br class="">
Oli.<br class="">
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