From PyMOLWiki
Revision as of 08:56, 25 October 2012 by Inchoate (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


This script will create a CGO circle with the origin at the specified X,Y,Z coordinates. Also, you can specify the radius and the colors. See the examples.

If you want to draw a circle around an object or selection, use circleSelection. If you want pure flexibility over your circle then use cgoCircle.

There are two functions here:


— creates a CGO circle at some user-specified location


—creates a circle around the named object or selection.


import math
import pymol
from pymol.cgo import *
import random

def cgoCircle(x, y, z, r=8.0, cr=1.0, cg=0.4, cb=0.8, w=2.0):
  Create a CGO circle

        x, y, z
          X, Y and Z coordinates of the origin

          Radius of the circle

        cr, cg, cb
          Color triplet, [r,g,b] where r,g,b are all [0.0,1.0].

          Line width of the circle

        the CGO object (it also loads it into PyMOL, too).

  x = float(x)
  y = float(y)
  z = float(z)
  r = abs(float(r))
  cr = abs(float(cr))
  cg = abs(float(cg))
  cb = abs(float(cb))
  w = float(w)

  obj = [ BEGIN, LINES, COLOR, cr, cg, cb ]
  for i in range(180):
        obj.append( VERTEX )
        obj.append(r*math.cos(i) + x )
        obj.append(r*math.sin(i) + y )
        obj.append( VERTEX )
        obj.append(r*math.cos(i+0.1) + x )
        obj.append(r*math.sin(i+0.1) + y )
  cName = cmd.get_unused_name("circle_")
  cmd.load_cgo( obj, cName )
  cmd.set("cgo_line_width", w, cName )
  return obj

def circleSelection( selName, r=None, cr=1.0, cg=0.4, cb=0.8, w=2.0 ):
  circleSelection -- draws a cgo circle around a given selection or object

          Name of the thing to encircle.

          Radius of circle.
          DEFAULT: This cript automatically defines the radius for you.  If
          you select one atom and the resultant circle is too small, then
          you can override the script's calculation of r and specify your own.

        cr, cg, cb
          red, green and blue coloring, each a value in the range [0.0, 1.0]

        The circle object.

  ((minX, minY, minZ), (maxX, maxY, maxZ)) = cmd.get_extent(selName)

  if r==None:
        r = max( [maxX-minX, maxY-minY, maxZ-minZ] )

  stored.coords = []
  cmd.iterate_state(1, selName, "stored.coords.append([x,y,z])")
  l = len(stored.coords)

  centerX = sum(map(lambda x: x[0], stored.coords)) / l
  centerY = sum(map(lambda x: x[1], stored.coords)) / l
  centerZ = sum(map(lambda x: x[2], stored.coords)) / l

  return cgoCircle( centerX, centerY, centerZ, r, cr, cg, cb, w )

cmd.extend( "cgoCircle", cgoCircle )
cmd.extend( "circleSelection", circleSelection )


  • Line width option
  • better circle naming