|Author(s)||Sean M. Law|
|This code has been put under version control in the project Pymol-script-repo|
In the case of movies or simulation trajectories, it is often useful to quickly jump between different frames but not necessarily in any order. This script allows the user to specify a list of frames and flipping through the set of frames is controlled by a user-defined keystroke (limited to those available through the Set Key command). This script is a nice tool for identifying different protein states from a simulation and can be used in conjunction with the Modevectors script in a very useful way by first characterizing the directionality of the movements (using Modevectors) and then visualizing the change directly using this script.
Note: This script also requires the Check Key script!
load the script using the run command
jump [frame1 [,...frameN [,sleep=0.1 [,x=1 [,key='pgdn']]]]]
jump 1, 10, 100 #This causes the movie to jump from frame 1 to frame 10 and finally to frame 100 each time the 'pgdn' key is pressed #Note that there is no limit to the number of frames that can be specified jump 1, 10, 100, 1000, key='F1' #This sets the hotkey to F1. When pressed, it will jump through the frames 1, 10, 100, 1000 respectively jump 1, 10, 100, sleep=0.01 #This does the same thing as the first example except that the pause between frames is 10x faster #One could consider the "sleep" option to be similar to the frame rate jump 1, 10, 100, x=10 #This does the same thing as the first example except that each press of the hotkey will #cause the script to run through the specified frames 10 times before stopping. #Note that you will not be able to control or exit the script during the 10 iterations!
from pymol import cmd import time def jump (*args, **kwargs): """ Author Sean M. Law University of Michigan seanlaw_(at)_umich_dot_edu """ keystroke='pgdn' for key in kwargs: if (key == "key"): keystroke=kwargs["key"] keystroke=check_key(keystroke) if (keystroke == None): return else: continue cmd.set_key(keystroke, jumpit, args, kwargs) return cmd.extend("jump", jump) def jumpit (*args, **kwargs): x=1 sleep=0.1 for key in kwargs: if (key == "sleep"): sleep=kwargs["sleep"] sleep=float(sleep) elif (key == "x"): x=kwargs["x"] x=int(x) else: continue args=list(args) for i in range (x): for j in range (len(args)): cmd.frame(int(args[j])) cmd.refresh() time.sleep(sleep) return cmd.extend("jumpit", jumpit)