On Jun 1, 2012, at 12:19 PM, Trina Manalo wrote:
Hello,
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?
Hi Trina, 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 "Python"): from Ramachandran import RamachandranPlot plt = RamachandranPlot(mdInfo['mol']) import os.path plt.figure.savefig(os.path.join(os.path.expanduser("~"), "rama", "rama %05d.png" % mdInfo['frame']), format="png") plt.destroy() Notes: (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: http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.save... (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 daily build! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu