[Chimera-users] editing Python saved sessions

Eric Pettersen pett at cgl.ucsf.edu
Mon May 22 17:35:20 PDT 2006

As per Elaine's mail, great cover!  As for the session issue, since  
the last production release I've completely redone session handling.   
There are no longer PDB files embedded in sessions.  Instead,  
structures are built directly by the session.  Also, attributes that  
are the same for all atoms (or residues/molecules) are recorded once  
instead of once per atom.  As a result, sessions are smaller, use  
less memory when restoring, and restore faster.  This new session  
code is in the 1.2224 snapshot release.  If you try out 1.2224 and  
you still can't get a newly-saved session to restore (i.e. a session  
that was written using 1.2224), then let me know and I'll investigate  
to see if there are further bottlenecks I can eliminate.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On May 22, 2006, at 4:17 PM, Jonathan Hilmer wrote:

> Notepad++ will do a great job of editing the .py files.  I've found
> that this is an extremely convenient way to accomplish certain tasks,
> such as precise alignment of multiple clipping planes.  However, you
> definitely have to know what you're looking for when digging through
> the files.
> On a related issue, I have a question regarding the saved sessions.
> In some of the viral capsid models I've created a saved session is
> enormous (about 60 megabytes) and fails to compile either
> automatically when loading the .py session or manually using the
> python.exe included with Chimera.  It seems to be a result of
> excessive explicit attribute assignments that I don't really care
> about (color etc) since they are easy enough to set once the model has
> loaded.
> Does anyone have any suggestions or experience with this issue?
> Jonathan
> PS: Check out the most recent issue of Science.  Although the editors
> chose the least visually impressive submission, non of the variations
> would have been possible without Chimera: great program.
>> Hello. My name is Anne Szklarski and I am a student at The College  
>> of New
>> Jersey. I was wondering if there was a way that the python files  
>> could be
>> modified in notepad. Does it require the Python software? The  
>> reason I ask
>> is because I have been renaming certain atoms in the .ent files using
>> notepad so that I may specifically select them in chimera. The only
>> problem with my current method is that I have to start the rendering
>> process from the beginning which is quite time consuming. So I was
>> wondering if there was a way that I could alter the chimera file  
>> directly
>> and not lose any of the colors, etc. that I have chosen. I  
>> appreciate any
>> information on this matter.
>> Thank you,
>> Anne Szklarski
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