My software notes

January 21, 2006

[pymol]color simple cartoon view (Chinese)

Filed under: pymol/ molmol — kpwu @ 4:06 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
  • 畫cartoon圖
    show cartoon, 1m58
  • 設定helix為紅色 (ss為secondary structure,h指 a-helix, 同理,l為loop, s為b-sheet)
    color red, ss h
  • 設定sheets顏色為orange
    color orange, ss s
  • 設定loop顏色為green
    color green, ss l+”
  • 設定cartoon的顯示為discrete colors,此時每段二級結構之間的顏色為獨立的狀態)
    set cartoon_discrete_colors, 1
  • 設定cartoon的顯示為highlight color,且highlight的顏色為yellow (1為black, 0為white,亦可自行定義顏色)
    set cartoon_highlight_color, yellow
  • Show fancy helices (Tcl/Tk GUI -> cartoon -> fancy helices check on)
    set cartoon_fancy_helices=1
  • zoom out view (負值為放大,正值為縮小)
    zoom 1m58, -15
  • 設定圖形輸出解析度
    ray 400,320
  • 輸出最後結果
    png 1m58-2.png

Last modified: 2004/04/26


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