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标题: pymol gromacs 轨迹　自动存储　画图　papa的儿子 [打印本页]
作者: meatball1982    时间: 2016-3-11 16:41
标题: pymol gromacs 轨迹　自动存储　画图　papa的儿子
  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. #
复制代码
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.


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