[Chimera-users] Saving sessions including maps?

Dougherty, Matthew T matthewd at bcm.edu
Fri Sep 11 14:29:24 PDT 2015

The viz package Amira has something similar called 'pack and go'.   And the video editing software Final Cut Pro has 'media manager', which provides more control.

It would be a useful option  to bundle the whole working directory, including pdfs, spreadsheets, manuscript drafts.

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.

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.

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.

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine

From: chimera-users-bounces at cgl.ucsf.edu <chimera-users-bounces at cgl.ucsf.edu> on behalf of Oliver Clarke <olibclarke at gmail.com>
Sent: Friday, September 11, 2015 3:04 PM
To: Tom Goddard
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Saving sessions including maps?

Thanks for the quick reply Tom, got it. Looking forward to Chimera 2!

One temporary work around I have thought about is the following alias:

#Save session with maps. saves in home dir with directory name same as session.
# Usage: save_session_dir session-name
# Don't use spaces or under_scores in session names.
alias ^save_session_dir volume # save ~/$1/map%d.mrc; save ~/$1/$1

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.

On Sep 11, 2015, at 6:54 PM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

Hi Oliver,

  This has long been a requested feature.


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.


On Sep 11, 2015, at 2:05 AM, Oliver Clarke wrote:

Hi all,

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?

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.

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.

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?


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