[chimera-dev] examples of 2-D plotting in plugins?
David A. C. Beck
dacb at u.washington.edu
Mon Nov 3 15:09:04 PST 2008
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:
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/tcl18.104.22.168/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
> 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
> 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 Pettersen
> UCSF Computer Graphics Lab
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