126 lines
4.1 KiB
Python
126 lines
4.1 KiB
Python
from pymol.cgo import *
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from pymol import cmd
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from chempy.cpv import normalize, cross_product, add, scale
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from math import sqrt
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# pore through a membrane
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radius = 19.0
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edge = 70.0
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sampling = 6
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depth = 20.0
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obj = []
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for z1 in [0.0, depth]:
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for basis in [ [ [ 1.0, 0.0, 0.0], [ 0.0, 1.0, 0.0], 0],
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[ [ 0.0, 1.0, 0.0], [ -1.0, 0.0, 0.0], 0],
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[ [-1.0, 0.0, 0.0], [ 0.0, -1.0, 0.0], 0],
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[ [ 0.0, -1.0, 0.0], [ 1.0, 0.0, 0.0], 0],
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[ [ 1.0, 0.0, 0.0], [ 0.0, 1.0, 0.0], 1],
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[ [ 0.0, 1.0, 0.0], [ -1.0, 0.0, 0.0], 1],
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[ [-1.0, 0.0, 0.0], [ 0.0, -1.0, 0.0], 1],
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[ [ 0.0, -1.0, 0.0], [ 1.0, 0.0, 0.0], 1],
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]:
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hand = basis[2]
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if hand:
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if z1 == 0.0:
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(x,y) = basis[0:2]
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else:
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(y,x) = basis[0:2]
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normal = normalize(cross_product(x,y))
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else:
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if z1 == 0.0:
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(y,x) = basis[0:2]
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else:
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(x,y) = basis[0:2]
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normal = normalize(cross_product(y,x))
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obj.extend( [BEGIN, TRIANGLE_STRIP] +
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[COLOR, 1.0, 1.0, 1.0] +
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[NORMAL] + normal )
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for i in range(sampling+1):
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x1 = edge
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y1 = edge*i/sampling
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vlen = sqrt(x1*x1+y1*y1)
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x0 = radius*x1/vlen
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y0 = radius*y1/vlen
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v0 = add( add( scale(x, x0 ), scale(y,y0) ), scale(normal,z1) )
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v1 = add( add( scale(x, x1 ), scale(y,y1) ), scale(normal,z1) )
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if hand:
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obj.extend( [ VERTEX ] + v0 + [ VERTEX ] + v1 )
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else:
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obj.extend( [ VERTEX ] + v1 + [ VERTEX ] + v0 )
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obj.extend( [END] )
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obj.extend( [BEGIN, TRIANGLE_STRIP] +
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[COLOR, 1.0, 1.0, 1.0])
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for i in range(sampling+1):
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x1 = edge
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y1 = edge*i/sampling
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vlen = sqrt(x1*x1+y1*y1)
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n0 = add( scale(x,-x1/vlen), scale(y, -y1/vlen) )
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x0 = radius*x1/vlen
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y0 = radius*y1/vlen
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v0 = add( scale(x, x0), scale(y,y0) )
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v1 = add( add( scale(x, x0), scale(y,y0) ), scale(normal,z1) )
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obj.extend( [ NORMAL] + n0 )
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if hand:
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obj.extend( [ VERTEX ] + v0 + [ VERTEX ] + v1 )
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else:
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obj.extend( [ VERTEX ] + v1 + [ VERTEX ] + v0 )
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obj.extend( [END] )
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obj.extend( [BEGIN, TRIANGLE_STRIP] +
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[COLOR, 1.0, 1.0, 1.0])
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for i in range(sampling+1):
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x1 = edge
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y1 = edge*i/sampling
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vlen = sqrt(x1*x1+y1*y1)
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n0 = scale(x, 1.0/edge)
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v0 = add( scale(x, x1), scale(y,y1) )
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v1 = add( add( scale(x, x1), scale(y,y1) ), scale(normal,z1) )
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obj.extend( [ NORMAL] + n0 )
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if not hand:
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obj.extend( [ VERTEX ] + v0 + [ VERTEX ] + v1 )
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else:
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obj.extend( [ VERTEX ] + v1 + [ VERTEX ] + v0 )
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obj.extend( [END] )
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# then we load it into PyMOL
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cmd.load_cgo(obj,'cgo06')
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# position haemolysin through pore
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if 1:
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cmd.fetch("7ahl")
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cmd.transform_selection("7ahl",
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(0.70349078502033213, 0.19033556773811347, -0.68474258132841503, -11.993190038310882,
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-0.15869362855324043, 0.98121371667870472, 0.10970571819737528, -29.939406659327624,
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0.69276001846262825, 0.03148755047390385, 0.72048024614206196, -26.250180846754432,
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0.0, 0.0, 0.0, 1.0))
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cmd.show_as("cartoon","7ahl")
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cmd.do("util.cbc")
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cmd.set_view((\
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-0.589197695, -0.440498680, 0.677344978,\
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0.574851871, -0.817646086, -0.031699535,\
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0.567794442, 0.370693058, 0.734975874,\
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0.000004128, -0.000099868, -651.343872070,\
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-4.874452114, 8.360315323, 11.387301445,\
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528.689147949, 773.963684082, 0.000000000 ))
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