[Chimera-users] Question about reopening morph ensembles

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 26 11:59:56 PDT 2010

On Apr 22, 2010, at 11:49 AM, Thomas Goddard wrote:

> Hi Andrew,
>  This problem with the MD movie interface not working with reloaded  
> sessions is in our bug database
> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/8245
> and has been noted by several other users.  Eric Pettersen has it  
> assigned a "low" priority which means it is unlikely to be fixed  
> this year.  It may be difficult to fix.  Eric is on vacation but may  
> have further comments when he returns.

Well, it is at low priority for a variety of reasons:

1) It is in fact of relatively low utility for actual molecular  
dynamics trajectories (especially compared to various other  
improvements I could make to that tool).  An MD user is typically not  
going to want to save what is basically a second copy of their  
trajectory data into a session, which is what would happen unless I do  
something pretty tricky during the session save.  Also, Chimera's  
session files aren't as efficient space-wise as the original files (in  
the two cases I tried the session file was 64-78% larger than the  
trajectory files).

2) The MD tool is old code that I didn't originally write and isn't  
well designed for session saving (or command-line use for that  
matter).  It is split into two modules that would both have to be  
saved and coordinated with each other and a lot of new code would need  
to be written to "revive" the graphical interface from a session file.

3) Other aspects of saving the GUI would be tricky, such as what to do  
about trajectories that haven't been fully loaded from their input  
files, but also such things as saving RMSD maps and occupancy  
volumes.  Since the latter didn't come from volume input files they  
don't get automatically saved into sessions (currently the user has to  
save each one of them into volume files first).

	I an not unwilling to do the work necessary here, but I think we as a  
team have to decide that it is worth pushing down some other priority  
item to do so.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

P.S. I'm adding this info to the Trac ticket.
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