讓PyMOL顯示XYZ軸

想要讓PyMOL顯示像VMD一樣有從原點出來的XYZ軸，參考PyMOLWiki上的文章《Axes》，修改程式碼儲存成axes.py。打開PyMOL以後執行下面的指令

• run axes.py
• axes
• axes(2)
• axes(3)

上面的三個指令都會畫出軸來，大小正比於小括號裡面的數字，結果如附的圖所示

Envelope proteins of Zika virus (PDB code: 5IRE)

axes.py的程式碼如下：

from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

def axes(size=1.0):    
    """
    DESCRIPTION:
    show the axes
    
    USAGE: the number is the size of the axes
        axes
        axes(2)
        axes(3)
    """
    
    w = 0.06 # cylinder width 
    l = 0.75 # cylinder length
    h = 0.25 # cone hight
    w, l, h = size*0.3, size*3.75, size*1.25
    d = w * 1.618 # cone base diameter

    obj = [CYLINDER, 0.0, 0.0, 0.0,   l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0,
           CYLINDER, 0.0, 0.0, 0.0, 0.0,   l, 0.0, w, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0,
           CYLINDER, 0.0, 0.0, 0.0, 0.0, 0.0,   l, w, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0,
           CONE,   l, 0.0, 0.0, h+l, 0.0, 0.0, d, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 
           CONE, 0.0,   l, 0.0, 0.0, h+l, 0.0, d, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0, 
           CONE, 0.0, 0.0,   l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0]

    #cyl_text(obj,plain,[-1.5,-1.5,-1.5],'O',0.2, axes=[[2,0,0],[0,2,0],[0,0,2]])
    cyl_text(obj,plain,[size*5.8, 0.     ,0.      ],'X', size*0.20, axes=[[size,0,0],[0,size,0],[0,0,size]])
    cyl_text(obj,plain,[0.      ,size*5.8,0.      ],'Y', size*0.20, axes=[[size,0,0],[0,size,0],[0,0,size]])
    cyl_text(obj,plain,[0.      ,0.      ,size*5.8],'Z', size*0.20, axes=[[size,0,0],[0,size,0],[0,0,size]])

    cmd.load_cgo(obj, 'axes')
    
cmd.extend('axes', axes) 

_EOF_