On Jun 4, 2012, at 2:42 PM, Anne Bowen wrote:

Hi,

I currently have a "Per-Frame Command" set up (in the MD Movie dialog) that finds the H bonds (findhbond makePseudobonds true lineWidth 2.0 color green intramodel true intermodel false selRestrict any) every frame of a trajectory. Whenever a hbond is detected, I would like to turn the entire structure a different color just for that frame, and then have it go back to being colored by heteroatom. Is there an easy way to accomplish this? I tried to look through the documentation to determine if "findhbond" could return true or false if an h bond was found and it did not seem like it was possible. Is the only way to do this to change the findhbond script itself? Any help or suggestions is greatly appreciated!

Hi Anne, You will have to resort to Python to do what you want to do here. Very simple Python, but Python nonetheless. The reason it can be simple is that there is a Python command named runCommand that allows you to execute regular Chimera commands and therefore the bulk of the script is just Python calls of commands you already know, with a little extra logic/glue to perform the test for the H-bonds and execute the corresponding color command. So first, in the "Per-Frame" dialog change the "Interpret script as" to "Python". Then put this in as your script: from chimera import runCommand runCommand("findhbond makePseudobonds true lineWidth 2.0 color green intramodel true intermodel false selRestrict any") if len(chimera.misc.getPseudoBondGroup("hydrogen bonds").pseudoBonds)

0: runCommand("color red") else: runCommand("~color; color byhet")

I chose red as the "other color"; change it to whatever you like. The "~color" is needed before the "color byhet" so that the carbon atoms will go to their non-red color. I'm guessing you'd like it if MD Movie's Analysis->Plot menu item allowed for plotting number of H-bonds? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu