My software notes

January 21, 2006

Advanced NMR data (PDB) presentations–ensemble view

Filed under: pymol/ molmol — kpwu @ 4:27 am


  • 從程式集開啟PyMOL
    Open PyMol
  • 載入pdb files, 可用指令模式或用工具列啟動
    load 1m58.pdb ( Use PyMOL Tcl/Tk GUI, File -> open -> 1m58.pdb)
  • 消去預先顯示的畫面
    hide all
  • 設定觀看畫面視窗
    viewport 640,480
  • 背景顏色為white
    bg_color white
  • 顯示全部的PDB (totally 15)
    set all_states, on
  • 用 line 表示結構
    show line, 1m58
  • 隱藏 side chain以及 back-bone上的O, NH
    cmd.hide(“((byres (1m58))&!n;ca,c,n)”)
    註: cmd.hide(“((byres (1m58))&!n;ca,c,n,o,h)”) 就表示單純hide side chain
  • 黑色表示backbone
    color black, 1m58
  • 改變 line width
    set line_width, 1.5
  • 輸出最後結果
    png 15-nmr-pdb.png


From pymol discussion mailing list (Jan 15, 2006)
Joel Tyndall provides detailing commands

  • To see them all at once:

load my_struct.pdb
set all_states

  • Or if you want them separated into individual objects:

unset all_states
split_states my_struct
dele my_struct

Last modified: 2004/06/28, 2006/01/21



  1. hi, hi, hi! Beautiful site.

    Comment by Petro — July 8, 2007 @ 10:11 pm | Reply

  2. hi, I have a question for you.
    When I load an ensemble of a protein, then I save the molecule, just only one (the first molecule) was save. I don’t know why?

    Comment by min — March 20, 2009 @ 8:12 am | Reply

  3. I don’t know how you did. What I can guess is you load 10 PDBs into pymol and save one selected PDB. You have to check the definition fro PDB site to know how to merge multiple coordinates in one PDB file.

    Comment by kpwu — March 20, 2009 @ 1:38 pm | Reply

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