Axes

Axes with text labels

# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
   CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
   CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
   CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
   ]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

Axes with nice cones

This script draws a simple cartesian coordinate system.

from pymol.cgo import *
from pymol import cmd

w = 0.06 # cylinder width 
l = 0.75 # cylinder length
h = 0.25 # cone hight
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]

cmd.load_cgo(obj, 'axes')

Axes which always stay in the lower left corner

from pymol import cmd
from chempy import cpv

class PutCenterCallback(object):
    prev_v = None

    def __init__(self, name, corner=0):
        self.name = name
        self.corner = corner
        self.cb_name = cmd.get_unused_name('_cb')

    def load(self):
        cmd.load_callback(self, self.cb_name)

    def __call__(self):
        if self.name not in cmd.get_names('objects'):
            import threading
            threading.Thread(None, cmd.delete, args=(self.cb_name,)).start()
            return

        v = cmd.get_view()
        if v == self.prev_v:
            return
        self.prev_v = v

        t = v[12:15]

        if self.corner:
            vp = cmd.get_viewport()
            R_mc = [v[0:3], v[3:6], v[6:9]]
            off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
            if self.corner in [2,3]:
                off_c[0] *= -1
            if self.corner in [3,4]:
                off_c[1] *= -1
            off_m = cpv.transform(R_mc, off_c)
            t = cpv.add(t, off_m)

        z = -v[11] / 30.0
        m = [z, 0, 0, 0, 0, z, 0, 0, 0, 0, z, 0, t[0] / z, t[1] / z, t[2] / z, 1]
        cmd.set_object_ttt(self.name, m)

def axes(name='axes'):
    '''
DESCRIPTION

    Puts coordinate axes to the lower left corner of the viewport.
    '''
    from pymol import cgo

    cmd.set('auto_zoom', 0)

    w = 0.06 # cylinder width
    l = 0.75 # cylinder length
    h = 0.25 # cone hight
    d = w * 1.618 # cone base diameter

    obj = [cgo.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,
           cgo.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,
           cgo.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,
           cgo.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,
           cgo.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,
           cgo.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]

    PutCenterCallback(name, 1).load()
    cmd.load_cgo(obj, name)

cmd.extend('axes', axes)