[Chimera-users] Question about animated Ramachandran plot
pett at cgl.ucsf.edu
Mon Jun 4 17:40:36 PDT 2012
On Jun 1, 2012, at 12:19 PM, Trina Manalo wrote:
> I would like to create an animated Ramachandran plot using an MD
> trajectory. One approach I've considered is using a per-frame script
> to save Ramachandran plot images (i.e., using the model panel, its
> possible to create a plot and then save the image as a png)
> Is there a way to do this using commands? Or is there an easier way
> to animate a plot of phi and psi angles over time?
Um, how good are you with Python? This is definitely a Python
thing. Here is a script you would use, after some modification, in
the MD Movie per-frame dialog (with "Interpret script as" set to
from Ramachandran import RamachandranPlot
plt = RamachandranPlot(mdInfo['mol'])
plt.figure.savefig(os.path.join(os.path.expanduser("~"), "rama", "rama
%05d.png" % mdInfo['frame']),
(1) You probably want to turn off looping before running the script.
(2) The script will save a series of PNG format images into a folder
named "rama" under your home directory. Make sure to create that
folder before running the script. The files will have names like
rama00005.png (for the fifth frame). If you want to change where the
images are saved or their names you need to modify the 'savefig' in
the script. If you know any Python it's simple. You may be able to
figure it out if you don't, but if you need help let me know. If you
want a format other than PNG or possibly other behaviors, the
documentation for the savefig command is here:
(3) You will need to get tomorrow's daily build to run the script
successfully because I had to fix two problems to get it to work.
There was a bug in the code that destroyed the Ramachandran plot
dialog after it was used (don't want a million plots on the screen!).
Also, the script was not being executed for the frame where it was
defined -- so if you defined it when frame 1 was showing you wouldn't
get a rama00001.png, the pngs would start with rama00002.png. Though
if looping was on you would eventually get a rama00001.png when it
looped around. This bug was introduced sometime between the 1.4.1 and
1.5.3 releases. Anyway, anybody running MD Movie scripts: get a
UCSF Computer Graphics Lab
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