pymol gromacs 轨迹 自动存储 画图 papa的儿子

meatball1982

1. #####################################
   
2. # outline
   
3. # use pymol to auto save a trj pdb into figures
   
4. #
   
5. # example :
   
6. # pymol -c Py_draw.py -- iamref.pdb iamtraj.pdb iamanme 3000 iamfigname
   
7. #####################################
   
8. import pymol
   
9. import cmd
   
10. import sys, time, os
    
11. #####################################
    
12. # inputs
    
13. # pdb      : a structure file. .pdb .gro
    
14. # trj      : a trajectory file. .pdb(multi frames), .trr
    
15. # name     : the name of the trj u import into pymol, it is anything u like
    
16. # ray_size : ray number, usually bigger, more clear
    
17. # fig_name : the output figure name
    
18. pdb = sys.argv[1]
    
19. trj = sys.argv[2]
    
20. name = sys.argv[3]
    
21. ray_size = sys.argv[4]
    
22. fig_name = sys.argv[5]
    
23. ####################################
    
24. # load and plot
    
25. cmd.load(pdb,name)# load reference structure
    
26. cmd.load(trj,name)# load traj file
    
27. cmd.show("cartoon",name)#use cartoon to plot pdb
    
28. cmd.hide("line",name)# hide the line
    
29. cmd.color("red","ss h")# set alpha red
    
30. cmd.color("yellow","ss s")# set beta  yellow
    
31. cmd.color("green","ss l+''")# set other green
    
32. cmd.set("ray_opaque_background","off")# background transpancy
    
33. for x in range(1,12,2) :# plot range for 1 to 12 int 1
    
34.         cmd.frame("%d" %x )
    
35.         cmd.zoom(name,state=-1)# zoom, show a big pdb in each frame
    
36.         cmd.ray(ray_size)# clearer
    
37.         cmd.png("fig_name"+str(x-1)+".png")# output fig
    
38. cmd.quit()# quit pymol
    
39. ####################################
    
40. # logs
    
41. # typed by : meatball1982@163.com
    
42. #
    

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有一个轨迹,　有一个ref的pdb,如何自动将轨迹中的每隔2frame的图存出来.