[Chimera-users] Question about reopening morph ensembles

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 26 12:24:23 PDT 2010

Hi Andrew,
As YZ mentioned earlier, you can access the whole morph trajectory in  
the saved session using the "coordset" command, it is just control via  
the MD Movie interface that is not available.  For me at least, this  
makes full session compatibility of MD Movie less urgent.  Starting  
with the saved session, you can still replay the trajectory with  
"coordset", and this could be done in a script along with movie  
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 26, 2010, at 11:59 AM, Eric Pettersen wrote:

> 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
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> P.S. I'm adding this info to the Trac ticket.

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