[chimera-dev] examples of 2-D plotting in plugins?

Eric Pettersen pett at cgl.ucsf.edu
Mon Nov 3 15:50:03 PST 2008

Hey, negative experiences are valuable to know about too!  The more  
info we have for making a decision, the better.  We do have practice  
with making recalcitrant builds bend to our will though. :-)


On Nov 3, 2008, at 3:09 PM, David A. C. Beck wrote:

> Sorry for the quick response, I can flesh it out in some more detail  
> if
> anyone is interested...
> We have used BLT2 to display 2D graphs from inside Chimera.  The  
> input are
> typically energies or other emissions as a function of simulation time
> from our simulation software (ilmm) that interfaces with Chimera.  I
> never found a way to update the graph in real time (even though we can
> pump the data in over a socket from the simulation code). Instead the
> Pmw.Blt.Graph object has to be reloaded.  There must be a way around
> this.  The graphs are ugly and not in any way acceptable for  
> publication.
> The experience of getting everything to build against the correct
> headers and python libraries was frustrating.  The distribution to
> machines in our lab is kludgy at best.  I've never gotten it working
> under Windows or Mac.  In case there is any doubt from my tone, we  
> really
> don't like the BLT solution.
> Some of my notes on getting it to work with an older version of  
> Chimera:
> BLT info:
> Configure command for BLT to w/ with Daggett Lab chimera installation:
> ./configure --prefix=/net/programs/chimera/lib --with-tkincls=/net/ 
> programs/chimera/include --with-tclincls=/net/programs/chimera/ 
> include --with-blt=/net/programs/chimera/lib --with-tcllibs=/net/ 
> programs/chimera/lib --with-tklibs=/net/programs/chimera/lib
> make install for BLT is broken, and must be finished by hand;  run  
> make install, copy the libraries (.so) from
> /var/tmp/chimeraBuild/build/foreign/tcl8.4.2.16/lib to /net/programs/ 
> chimera/lib, then move the /net/programs/chimera/lib/blt2.4  
> directory into /net/programs/chimera/lib/tcl8.4
> it seems that the stuff in /var/tmp/chimeraBuild/build/foriegn...  
> has to be there for this to work
> --
> David A. C. Beck, Ph.D.
> dacb at u.washington.edu
> Valerie Daggett Laboratory
> University of Washington, Seattle
> On Mon, 3 Nov 2008, Eric Pettersen wrote:
>> FYI, the last paragraph of my reply below may be of general  
>> interest to
>> developers interested in plotting data...
>> On Oct 31, 2008, at 10:09 AM, Randy Heiland wrote:
>>> Hi gang,
>>> For one of the Chimera plugins that I now maintain, I'm considering
>>> eliminating the use of matplotlib and wondering if Chimera's innards
>>> are capable of doing what I want.  For starters, are there any
>>> example plugins, etc that demonstrate how one could do simple
>>> plotting and simple (image) contours?  In addition, I'd need to
>>> handle mouse events, e.g. to retrieve x,y positions on the contour
>>> image.
>> Hi Randy,
>> 	I'm thinking that what Chimera currently provides will not be an
>> adequate replacement for the capabilities of matplotlib that  
>> NLOPredict uses.
>> Aside from the basic Tk widgets themselves (the most salient of  
>> which is
>> Canvas) the only relevant widgets I can think of is an interactive  
>> histogram
>> widget in CGLtk.Histogram, and a basic line/point plotting widget  
>> available
>> through Scientific.TkWidgets.TkPlotCanvas
>> (Scientific.TkWidgets.TkPlotCanvas).
>> 	But I think NLOPredict needs interactive contour and bar graphs.  As
>> long as you can generate the contour image yourself somehow, I  
>> think you can
>> pretty easily gin up an interactive contour plot using the Image  
>> item of
>> Tk.Canvas.  As for the bar graph, would BLT (A User's Guide to  
>> Pmw.Blt)
>> provide enough functionality if we decided to provide that?  It  
>> seems to
>> provide bar charts (A complete reference to the Pmw.Blt plot  
>> widget).  It
>> also might or might not be easier for you to provide BLT for  
>> NLOPredict as a
>> stopgap measure.
>> 	So the Chimera developers will be discussing possibly providing some
>> kind of plotting library at our next weekly meeting.  Clearly,  
>> matplotlib is
>> the "Cadillac" of plotting libraries.  And like a Cadillac it has the
>> downside of large size -- probably in the range of 60-80MB before
>> compression.  It also has the drawback of depending on a lot of other
>> packages which we would also have to include and port to all our  
>> supported
>> platforms, including 64-bit versions thereof.  So I guess the  
>> question is
>> whether we could get away with including something smaller like  
>> BLT, which we
>> would also be able to deploy more quickly due to the lower effort  
>> involved,
>> or do people really need the unique capabilities of matplotlib?   
>> Anybody?
>> --Eric
>>                      Eric Pettersen
>>                      UCSF Computer Graphics Lab
>>                      http://www.cgl.ucsf.edu
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