Skip to content

Instantly share code, notes, and snippets.

@sunhwan

sunhwan/arrow.py

Created November 3, 2011 17:01
Show Gist options
  • Save sunhwan/1337055 to your computer and use it in GitHub Desktop.
Save sunhwan/1337055 to your computer and use it in GitHub Desktop.
Download ZIP
draw helical axis in pymol
Raw
arrow.py
from pymol import cmd
from pymol.cgo import *
from math import *
#
# Some functions to allow drawing arrows (vectors) in Pymol
# In need of proper documentation...
#
# Please don't distribute (parts of) this file, without credits
#
# (c)2006 Tsjerk A. Wassenaar, PhD, University of Utrecht
#
# t s j e r k w .at. g m a i l .dot. c o m
# http://nmr.chem.uu.nl/~tsjerk/
#
def t( X ):
if not X: return X
Y = []
for i in range( len( X[0] ) ):
Y.append( [] )
for j in X:
Y[i].append( j[i] )
return Y
def v_add( a, b ): return ( a[0]+b[0], a[1]+b[1], a[2]+b[2] )
def v_sub( a, b ): return ( a[0]-b[0], a[1]-b[1], a[2]-b[2] )
def vecprod( a, b ): return ( a[1]*b[2]-a[2]*b[1],
a[2]*b[0]-a[0]*b[2], a[0]*b[1]-a[1]*b[0] )
def inprod( a, b=None ):
if b: return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]
else: return a[0]*a[0] + a[1]*a[1] + a[2]*a[2]
def svmult( s, a ): return ( s*a[0], s*a[1], s*a[2] )
def norm( a ): return svmult( 1/sqrt(inprod( a )), a )
def mvmult( R, x ):
y = []
for i in R: y.append( inprod( i, x ) )
return tuple(y)
def mv_add( X, a ):
Y = []
for i in X:
Y.append( v_add( i, a ) )
return Y
def mmmult( R, X ):
Y = []
for i in X: Y.append( mvmult( R, i ) )
return Y
def smatrix( v ): return [[ v[0], 0, 0 ], [ 0, v[1], 0 ], [ 0, 0, v[2] ]]
def rmatrix( v ):
cosx, sinx = cos( v[0] ), sin( v[0] )
cosy, siny = cos( v[1] ), sin( v[1] )
cosz, sinz = cos( v[2] ), sin( v[2] )
return mmmult( mmmult( [[1,0,0],[0,cosx,-sinx],[0,sinx,cosx]],
[[cosy,0,-siny],[0,1,0],[siny,0,cosy]] ),
[[cosz,-sinz,0],[sinz,cosz,0],[0,0,1]] )
def block( i, dphi ):
ddphi = 0.25*dphi
phi0 = i*dphi
phi1 = phi0+ddphi
phi2 = phi1+ddphi
phi3 = phi2+ddphi
phi4 = phi3+ddphi
sqrt2 = sqrt(2)
return [ (-0.5*sqrt2,-0.5*sqrt2*cos(phi2),0.5*sqrt2*sin(phi2)),
(1,0,0),
(0,cos(phi0),-sin(phi0)),
(0,cos(phi1),-sin(phi1)),
(0,cos(phi2),-sin(phi2)),
(0,cos(phi3),-sin(phi3)),
(0,cos(phi4),-sin(phi4))
]
def cgo_triangle_fan( X ):
Y = []
while ( X ):
i = X.pop(0)
Y.extend( [ NORMAL, i[0], i[1], i[2], ] )
for i in range( 6 ):
i = X.pop(0)
Y.extend( [ VERTEX, i[0], i[1], i[2], ] )
return Y
def cgo_arrow1( S, E, r=0.2, hr=0.4, hl=1.0 ):
P0 = S
D = v_sub( E, S )
DL = inprod( D, D )
P1 = v_add( S, svmult( (DL-hl)/DL, D ) )
P2 = E
# Define a vector orthogonal to P1-P0
V = v_sub( P1, P0 )
V = norm( V )
if V[2] != 0:
A = ( 1, 1, -(V[0]+V[1])/V[2] )
elif V[1] != 0:
A = ( 1, -V[0]/V[1], 0 )
else:
A = ( 0, -V[0], 0 )
A = norm( A )
B = vecprod( V, A )
print (inprod(V), inprod(B), inprod(A))
R = t([ svmult( hl,V ), svmult( hr,A ), svmult( hr,B ) ])
# Define the transformation matrix (scale and rotation)
#C = v_sub( P2, P1 )
#scale = ( hl, hr, hr )
#rotate = ( 0, acos( C[0]/sqrt(C[0]**2+C[2]**2) ), acos( C[0]/sqrt(C[0]**2+C[1]**2) ) )
#R = mmmult( smatrix( scale ), rmatrix( rotate ) )
obj = [
CYLINDER, S[0], S[1], S[2], P1[0], P1[1], P1[2], r, 1, 1, 1, 1, 1, 1,
COLOR, 1, 0, 0,
BEGIN, TRIANGLE_FAN ]
N = 10
dphi = 2*pi/N
crds = []
for i in range(N+1):
crds.extend( block( i, dphi ) )
crds = mv_add( mmmult( R, crds ), P1 )
obj.extend( cgo_triangle_fan( crds ) )
obj.extend( [ END, ] )
return obj
def cgo_arrow( S, E, r=0.2, hr=0.4, hl=1.0, name="arrow", state=1 ):
obj = cgo_arrow1( S, E, r=r, hr=hr, hl=hl )
cmd.load_cgo( obj, name, state )
def cgo_arrows( X, r=0.2, hr=0.4, hl=1.0, name="arrow", state=1 ):
obj = []
for i in X:
obj.extend( cgo_arrow1( (i[0], i[1], i[2]), (i[3], i[4],
i[5]), r=r, hr=hr, hl=hl ) )
cmd.load_cgo( obj, name, state )
Raw
ga.pdb
ATOM 1 C CHO 0 0.753 2.416 -0.575 1.00 0.00 PROA C
ATOM 2 O CHO 0 0.556 2.869 -1.731 1.00 0.00 PROA O
ATOM 3 HA CHO 0 0.128 2.571 0.316 1.00 0.00 PROA H
ATOM 4 N VAL 1 1.956 1.845 -0.269 1.00 0.00 PROA N
ATOM 5 CA VAL 1 2.873 1.222 -1.156 1.00 0.00 PROA C
ATOM 6 C VAL 1 2.735 -0.302 -0.890 1.00 0.00 PROA C
ATOM 7 O VAL 1 3.029 -0.786 0.243 1.00 0.00 PROA O
ATOM 8 CB VAL 1 4.241 1.735 -0.760 1.00 0.00 PROA C
ATOM 9 CG1 VAL 1 5.288 1.181 -1.652 1.00 0.00 PROA C
ATOM 10 CG2 VAL 1 4.420 3.303 -0.691 1.00 0.00 PROA C
ATOM 11 HN VAL 1 2.176 1.628 0.679 1.00 0.00 PROA H
ATOM 12 HA VAL 1 2.650 1.436 -2.190 1.00 0.00 PROA H
ATOM 13 HB VAL 1 4.323 1.396 0.295 1.00 0.00 PROA H
ATOM 14 HG11 VAL 1 6.322 1.381 -1.301 1.00 0.00 PROA H
ATOM 15 HG12 VAL 1 5.211 0.083 -1.803 1.00 0.00 PROA H
ATOM 16 HG13 VAL 1 5.167 1.659 -2.648 1.00 0.00 PROA H
ATOM 17 HG21 VAL 1 5.452 3.499 -0.329 1.00 0.00 PROA H
ATOM 18 HG22 VAL 1 3.654 3.773 -0.039 1.00 0.00 PROA H
ATOM 19 HG23 VAL 1 4.410 3.703 -1.728 1.00 0.00 PROA H
ATOM 20 N GLY 2 2.238 -1.109 -1.872 1.00 0.00 PROA N
ATOM 21 CA GLY 2 2.202 -2.578 -1.748 1.00 0.00 PROA C
ATOM 22 C GLY 2 1.165 -3.246 -2.639 1.00 0.00 PROA C
ATOM 23 O GLY 2 1.145 -3.047 -3.848 1.00 0.00 PROA O
ATOM 24 HN GLY 2 2.024 -0.776 -2.786 1.00 0.00 PROA H
ATOM 25 HA1 GLY 2 2.012 -2.793 -0.707 1.00 0.00 PROA H
ATOM 26 HA2 GLY 2 3.203 -2.888 -2.009 1.00 0.00 PROA H
ATOM 27 N ALA 3 0.245 -3.976 -1.961 1.00 0.00 PROA N
ATOM 28 CA ALA 3 -0.839 -4.522 -2.740 1.00 0.00 PROA C
ATOM 29 C ALA 3 -2.189 -3.996 -2.350 1.00 0.00 PROA C
ATOM 30 O ALA 3 -2.702 -4.112 -1.255 1.00 0.00 PROA O
ATOM 31 CB ALA 3 -0.942 -6.030 -2.474 1.00 0.00 PROA C
ATOM 32 HN ALA 3 0.389 -4.206 -1.002 1.00 0.00 PROA H
ATOM 33 HA ALA 3 -0.777 -4.318 -3.799 1.00 0.00 PROA H
ATOM 34 HB1 ALA 3 -0.077 -6.609 -2.863 1.00 0.00 PROA H
ATOM 35 HB2 ALA 3 -0.830 -6.221 -1.385 1.00 0.00 PROA H
ATOM 36 HB3 ALA 3 -1.867 -6.420 -2.950 1.00 0.00 PROA H
ATOM 37 N LED 4 -2.934 -3.436 -3.363 1.00 0.00 PROA N
ATOM 38 CA LED 4 -4.253 -2.878 -3.093 1.00 0.00 PROA C
ATOM 39 C LED 4 -4.427 -1.684 -3.948 1.00 0.00 PROA C
ATOM 40 O LED 4 -4.424 -1.729 -5.156 1.00 0.00 PROA O
ATOM 41 CB LED 4 -5.356 -3.822 -3.419 1.00 0.00 PROA C
ATOM 42 CG LED 4 -6.854 -3.294 -3.288 1.00 0.00 PROA C
ATOM 43 CD1 LED 4 -7.117 -2.582 -1.954 1.00 0.00 PROA C
ATOM 44 CD2 LED 4 -7.430 -2.353 -4.330 1.00 0.00 PROA C
ATOM 45 HN LED 4 -2.646 -3.317 -4.310 1.00 0.00 PROA H
ATOM 46 HA LED 4 -4.229 -2.520 -2.074 1.00 0.00 PROA H
ATOM 47 HB1 LED 4 -5.289 -4.207 -4.459 1.00 0.00 PROA H
ATOM 48 HB2 LED 4 -5.287 -4.676 -2.713 1.00 0.00 PROA H
ATOM 49 HG LED 4 -7.489 -4.206 -3.301 1.00 0.00 PROA H
ATOM 50 HD11 LED 4 -6.537 -1.649 -1.789 1.00 0.00 PROA H
ATOM 51 HD12 LED 4 -8.211 -2.389 -1.911 1.00 0.00 PROA H
ATOM 52 HD13 LED 4 -6.913 -3.181 -1.041 1.00 0.00 PROA H
ATOM 53 HD21 LED 4 -8.541 -2.348 -4.335 1.00 0.00 PROA H
ATOM 54 HD22 LED 4 -7.147 -2.699 -5.347 1.00 0.00 PROA H
ATOM 55 HD23 LED 4 -6.983 -1.338 -4.273 1.00 0.00 PROA H
ATOM 56 N ALA 5 -4.525 -0.514 -3.315 1.00 0.00 PROA N
ATOM 57 CA ALA 5 -4.485 0.747 -4.033 1.00 0.00 PROA C
ATOM 58 C ALA 5 -3.288 1.577 -3.618 1.00 0.00 PROA C
ATOM 59 O ALA 5 -2.762 1.582 -2.513 1.00 0.00 PROA O
ATOM 60 CB ALA 5 -5.764 1.563 -3.715 1.00 0.00 PROA C
ATOM 61 HN ALA 5 -4.596 -0.453 -2.323 1.00 0.00 PROA H
ATOM 62 HA ALA 5 -4.272 0.603 -5.082 1.00 0.00 PROA H
ATOM 63 HB1 ALA 5 -5.669 2.498 -4.309 1.00 0.00 PROA H
ATOM 64 HB2 ALA 5 -6.760 1.105 -3.894 1.00 0.00 PROA H
ATOM 65 HB3 ALA 5 -5.633 1.945 -2.680 1.00 0.00 PROA H
ATOM 66 N VAD 6 -2.701 2.376 -4.539 1.00 0.00 PROA N
ATOM 67 CA VAD 6 -1.714 3.368 -4.390 1.00 0.00 PROA C
ATOM 68 C VAD 6 -0.638 3.124 -5.354 1.00 0.00 PROA C
ATOM 69 O VAD 6 -0.825 3.346 -6.578 1.00 0.00 PROA O
ATOM 70 CB VAD 6 -2.110 4.825 -4.445 1.00 0.00 PROA C
ATOM 71 CG1 VAD 6 -3.106 5.002 -3.278 1.00 0.00 PROA C
ATOM 72 CG2 VAD 6 -1.024 5.832 -4.211 1.00 0.00 PROA C
ATOM 73 HN VAD 6 -2.970 2.153 -5.472 1.00 0.00 PROA H
ATOM 74 HA VAD 6 -1.357 3.243 -3.378 1.00 0.00 PROA H
ATOM 75 HB VAD 6 -2.695 5.072 -5.357 1.00 0.00 PROA H
ATOM 76 HG11 VAD 6 -3.933 4.263 -3.349 1.00 0.00 PROA H
ATOM 77 HG12 VAD 6 -3.454 6.057 -3.268 1.00 0.00 PROA H
ATOM 78 HG13 VAD 6 -2.606 4.768 -2.315 1.00 0.00 PROA H
ATOM 79 HG21 VAD 6 -0.632 5.660 -3.186 1.00 0.00 PROA H
ATOM 80 HG22 VAD 6 -1.460 6.851 -4.129 1.00 0.00 PROA H
ATOM 81 HG23 VAD 6 -0.145 5.872 -4.890 1.00 0.00 PROA H
ATOM 82 N VAL 7 0.506 2.625 -4.814 1.00 0.00 PROA N
ATOM 83 CA VAL 7 1.676 2.327 -5.576 1.00 0.00 PROA C
ATOM 84 C VAL 7 2.014 0.914 -5.282 1.00 0.00 PROA C
ATOM 85 O VAL 7 1.913 0.388 -4.184 1.00 0.00 PROA O
ATOM 86 CB VAL 7 2.827 3.250 -5.143 1.00 0.00 PROA C
ATOM 87 CG1 VAL 7 3.909 3.318 -6.221 1.00 0.00 PROA C
ATOM 88 CG2 VAL 7 2.366 4.603 -4.697 1.00 0.00 PROA C
ATOM 89 HN VAL 7 0.591 2.654 -3.821 1.00 0.00 PROA H
ATOM 90 HA VAL 7 1.519 2.527 -6.625 1.00 0.00 PROA H
ATOM 91 HB VAL 7 3.267 2.798 -4.228 1.00 0.00 PROA H
ATOM 92 HG11 VAL 7 4.128 2.287 -6.573 1.00 0.00 PROA H
ATOM 93 HG12 VAL 7 3.515 3.869 -7.101 1.00 0.00 PROA H
ATOM 94 HG13 VAL 7 4.836 3.699 -5.741 1.00 0.00 PROA H
ATOM 95 HG21 VAL 7 1.868 4.556 -3.706 1.00 0.00 PROA H
ATOM 96 HG22 VAL 7 1.787 5.148 -5.473 1.00 0.00 PROA H
ATOM 97 HG23 VAL 7 3.297 5.182 -4.513 1.00 0.00 PROA H
ATOM 98 N VAD 8 2.415 0.167 -6.285 1.00 0.00 PROA N
ATOM 99 CA VAD 8 2.835 -1.218 -6.205 1.00 0.00 PROA C
ATOM 100 C VAD 8 1.981 -2.007 -7.227 1.00 0.00 PROA C
ATOM 101 O VAD 8 1.918 -1.665 -8.414 1.00 0.00 PROA O
ATOM 102 CB VAD 8 4.251 -1.349 -6.496 1.00 0.00 PROA C
ATOM 103 CG1 VAD 8 5.190 -0.430 -5.763 1.00 0.00 PROA C
ATOM 104 CG2 VAD 8 4.759 -2.792 -6.340 1.00 0.00 PROA C
ATOM 105 HN VAD 8 2.483 0.681 -7.136 1.00 0.00 PROA H
ATOM 106 HA VAD 8 2.643 -1.739 -5.278 1.00 0.00 PROA H
ATOM 107 HB VAD 8 4.293 -1.003 -7.551 1.00 0.00 PROA H
ATOM 108 HG11 VAD 8 6.231 -0.587 -6.118 1.00 0.00 PROA H
ATOM 109 HG12 VAD 8 5.284 -0.667 -4.682 1.00 0.00 PROA H
ATOM 110 HG13 VAD 8 4.890 0.636 -5.852 1.00 0.00 PROA H
ATOM 111 HG21 VAD 8 4.282 -3.432 -7.114 1.00 0.00 PROA H
ATOM 112 HG22 VAD 8 4.609 -3.165 -5.305 1.00 0.00 PROA H
ATOM 113 HG23 VAD 8 5.835 -2.860 -6.606 1.00 0.00 PROA H
ATOM 114 N TRP 9 1.349 -3.093 -6.734 1.00 0.00 PROA N
ATOM 115 CA TRP 9 0.362 -3.827 -7.500 1.00 0.00 PROA C
ATOM 116 C TRP 9 -1.103 -3.588 -7.134 1.00 0.00 PROA C
ATOM 117 O TRP 9 -1.459 -3.385 -5.982 1.00 0.00 PROA O
ATOM 118 CB TRP 9 0.848 -5.348 -7.461 1.00 0.00 PROA C
ATOM 119 CG TRP 9 -0.072 -6.407 -8.023 1.00 0.00 PROA C
ATOM 120 CD1 TRP 9 -0.233 -6.903 -9.327 1.00 0.00 PROA C
ATOM 121 CD2 TRP 9 -1.052 -7.017 -7.219 1.00 0.00 PROA C
ATOM 122 CE2 TRP 9 -1.742 -7.880 -8.117 1.00 0.00 PROA C
ATOM 123 CE3 TRP 9 -1.387 -6.993 -5.830 1.00 0.00 PROA C
ATOM 124 NE1 TRP 9 -1.265 -7.740 -9.361 1.00 0.00 PROA N
ATOM 125 CZ2 TRP 9 -2.751 -8.722 -7.689 1.00 0.00 PROA C
ATOM 126 CZ3 TRP 9 -2.473 -7.843 -5.438 1.00 0.00 PROA C
ATOM 127 CH2 TRP 9 -3.020 -8.755 -6.311 1.00 0.00 PROA C
ATOM 128 HN TRP 9 1.534 -3.417 -5.809 1.00 0.00 PROA H
ATOM 129 HA TRP 9 0.398 -3.478 -8.521 1.00 0.00 PROA H
ATOM 130 HB1 TRP 9 1.767 -5.279 -8.081 1.00 0.00 PROA H
ATOM 131 HB2 TRP 9 1.192 -5.558 -6.426 1.00 0.00 PROA H
ATOM 132 HD1 TRP 9 0.356 -6.571 -10.169 1.00 0.00 PROA H
ATOM 133 HE1 TRP 9 -1.635 -8.154 -10.164 1.00 0.00 PROA H
ATOM 134 HE3 TRP 9 -0.949 -6.253 -5.177 1.00 0.00 PROA H
ATOM 135 HZ2 TRP 9 -3.353 -9.271 -8.397 1.00 0.00 PROA H
ATOM 136 HZ3 TRP 9 -2.697 -7.915 -4.384 1.00 0.00 PROA H
ATOM 137 HH2 TRP 9 -3.814 -9.387 -5.944 1.00 0.00 PROA H
ATOM 138 N LED 10 -1.966 -3.629 -8.098 1.00 0.00 PROA N
ATOM 139 CA LED 10 -3.406 -3.485 -7.985 1.00 0.00 PROA C
ATOM 140 C LED 10 -3.832 -2.198 -8.608 1.00 0.00 PROA C
ATOM 141 O LED 10 -3.684 -1.999 -9.815 1.00 0.00 PROA O
ATOM 142 CB LED 10 -3.971 -4.632 -8.759 1.00 0.00 PROA C
ATOM 143 CG LED 10 -5.472 -4.716 -8.859 1.00 0.00 PROA C
ATOM 144 CD1 LED 10 -5.752 -6.110 -9.469 1.00 0.00 PROA C
ATOM 145 CD2 LED 10 -6.130 -4.537 -7.440 1.00 0.00 PROA C
ATOM 146 HN LED 10 -1.623 -3.695 -9.032 1.00 0.00 PROA H
ATOM 147 HA LED 10 -3.656 -3.454 -6.935 1.00 0.00 PROA H
ATOM 148 HB1 LED 10 -3.576 -4.589 -9.796 1.00 0.00 PROA H
ATOM 149 HB2 LED 10 -3.516 -5.529 -8.286 1.00 0.00 PROA H
ATOM 150 HG LED 10 -5.874 -3.943 -9.549 1.00 0.00 PROA H
ATOM 151 HD11 LED 10 -6.751 -6.087 -9.955 1.00 0.00 PROA H
ATOM 152 HD12 LED 10 -5.048 -6.250 -10.317 1.00 0.00 PROA H
ATOM 153 HD13 LED 10 -5.622 -6.892 -8.690 1.00 0.00 PROA H
ATOM 154 HD21 LED 10 -5.775 -3.622 -6.918 1.00 0.00 PROA H
ATOM 155 HD22 LED 10 -5.835 -5.368 -6.765 1.00 0.00 PROA H
ATOM 156 HD23 LED 10 -7.230 -4.638 -7.553 1.00 0.00 PROA H
ATOM 157 N TRP 11 -4.333 -1.236 -7.889 1.00 0.00 PROA N
ATOM 158 CA TRP 11 -4.837 0.013 -8.390 1.00 0.00 PROA C
ATOM 159 C TRP 11 -3.853 1.201 -8.243 1.00 0.00 PROA C
ATOM 160 O TRP 11 -3.207 1.340 -7.139 1.00 0.00 PROA O
ATOM 161 CB TRP 11 -6.172 0.511 -7.863 1.00 0.00 PROA C
ATOM 162 CG TRP 11 -7.383 -0.255 -8.204 1.00 0.00 PROA C
ATOM 163 CD1 TRP 11 -7.550 -1.027 -9.296 1.00 0.00 PROA C
ATOM 164 CD2 TRP 11 -8.511 -0.366 -7.342 1.00 0.00 PROA C
ATOM 165 CE2 TRP 11 -9.423 -1.285 -7.916 1.00 0.00 PROA C
ATOM 166 CE3 TRP 11 -8.817 0.173 -6.123 1.00 0.00 PROA C
ATOM 167 NE1 TRP 11 -8.761 -1.763 -9.065 1.00 0.00 PROA N
ATOM 168 CZ2 TRP 11 -10.741 -1.490 -7.473 1.00 0.00 PROA C
ATOM 169 CZ3 TRP 11 -10.097 0.000 -5.547 1.00 0.00 PROA C
ATOM 170 CH2 TRP 11 -10.945 -0.904 -6.200 1.00 0.00 PROA C
ATOM 171 HN TRP 11 -4.484 -1.434 -6.924 1.00 0.00 PROA H
ATOM 172 HA TRP 11 -5.114 -0.105 -9.427 1.00 0.00 PROA H
ATOM 173 HB1 TRP 11 -6.143 0.621 -6.758 1.00 0.00 PROA H
ATOM 174 HB2 TRP 11 -6.232 1.550 -8.250 1.00 0.00 PROA H
ATOM 175 HD1 TRP 11 -6.871 -1.163 -10.125 1.00 0.00 PROA H
ATOM 176 HE1 TRP 11 -9.189 -2.342 -9.724 1.00 0.00 PROA H
ATOM 177 HE3 TRP 11 -8.203 0.933 -5.664 1.00 0.00 PROA H
ATOM 178 HZ2 TRP 11 -11.400 -2.209 -7.937 1.00 0.00 PROA H
ATOM 179 HZ3 TRP 11 -10.254 0.423 -4.566 1.00 0.00 PROA H
ATOM 180 HH2 TRP 11 -11.916 -1.014 -5.739 1.00 0.00 PROA H
ATOM 181 N LED 12 -3.694 2.059 -9.260 1.00 0.00 PROA N
ATOM 182 CA LED 12 -3.014 3.336 -9.010 1.00 0.00 PROA C
ATOM 183 C LED 12 -1.867 3.452 -9.976 1.00 0.00 PROA C
ATOM 184 O LED 12 -2.083 3.727 -11.188 1.00 0.00 PROA O
ATOM 185 CB LED 12 -3.908 4.538 -9.291 1.00 0.00 PROA C
ATOM 186 CG LED 12 -5.219 4.592 -8.450 1.00 0.00 PROA C
ATOM 187 CD1 LED 12 -5.026 4.440 -6.936 1.00 0.00 PROA C
ATOM 188 CD2 LED 12 -5.939 5.916 -8.821 1.00 0.00 PROA C
ATOM 189 HN LED 12 -4.201 1.889 -10.101 1.00 0.00 PROA H
ATOM 190 HA LED 12 -2.657 3.403 -7.993 1.00 0.00 PROA H
ATOM 191 HB1 LED 12 -3.429 5.526 -9.116 1.00 0.00 PROA H
ATOM 192 HB2 LED 12 -4.199 4.558 -10.363 1.00 0.00 PROA H
ATOM 193 HG LED 12 -5.967 3.872 -8.846 1.00 0.00 PROA H
ATOM 194 HD11 LED 12 -4.326 5.199 -6.526 1.00 0.00 PROA H
ATOM 195 HD12 LED 12 -5.971 4.676 -6.402 1.00 0.00 PROA H
ATOM 196 HD13 LED 12 -4.617 3.455 -6.623 1.00 0.00 PROA H
ATOM 197 HD21 LED 12 -5.857 6.046 -9.921 1.00 0.00 PROA H
ATOM 198 HD22 LED 12 -6.956 5.883 -8.376 1.00 0.00 PROA H
ATOM 199 HD23 LED 12 -5.295 6.675 -8.325 1.00 0.00 PROA H
ATOM 200 N TRP 13 -0.639 3.292 -9.558 1.00 0.00 PROA N
ATOM 201 CA TRP 13 0.526 3.509 -10.374 1.00 0.00 PROA C
ATOM 202 C TRP 13 1.545 2.357 -10.093 1.00 0.00 PROA C
ATOM 203 O TRP 13 1.989 2.160 -8.986 1.00 0.00 PROA O
ATOM 204 CB TRP 13 1.165 4.877 -10.106 1.00 0.00 PROA C
ATOM 205 CG TRP 13 0.443 6.130 -10.493 1.00 0.00 PROA C
ATOM 206 CD1 TRP 13 0.224 6.551 -11.786 1.00 0.00 PROA C
ATOM 207 CD2 TRP 13 -0.571 6.818 -9.698 1.00 0.00 PROA C
ATOM 208 CE2 TRP 13 -1.242 7.726 -10.561 1.00 0.00 PROA C
ATOM 209 CE3 TRP 13 -0.953 6.823 -8.310 1.00 0.00 PROA C
ATOM 210 NE1 TRP 13 -0.694 7.579 -11.813 1.00 0.00 PROA N
ATOM 211 CZ2 TRP 13 -2.289 8.429 -10.104 1.00 0.00 PROA C
ATOM 212 CZ3 TRP 13 -2.063 7.592 -7.844 1.00 0.00 PROA C
ATOM 213 CH2 TRP 13 -2.775 8.406 -8.775 1.00 0.00 PROA C
ATOM 214 HN TRP 13 -0.531 3.238 -8.569 1.00 0.00 PROA H
ATOM 215 HA TRP 13 0.210 3.353 -11.395 1.00 0.00 PROA H
ATOM 216 HB1 TRP 13 1.478 4.947 -9.042 1.00 0.00 PROA H
ATOM 217 HB2 TRP 13 2.109 4.911 -10.691 1.00 0.00 PROA H
ATOM 218 HD1 TRP 13 0.850 6.304 -12.630 1.00 0.00 PROA H
ATOM 219 HE1 TRP 13 -1.143 7.953 -12.594 1.00 0.00 PROA H
ATOM 220 HE3 TRP 13 -0.392 6.162 -7.667 1.00 0.00 PROA H
ATOM 221 HZ2 TRP 13 -2.701 9.179 -10.763 1.00 0.00 PROA H
ATOM 222 HZ3 TRP 13 -2.259 7.621 -6.783 1.00 0.00 PROA H
ATOM 223 HH2 TRP 13 -3.638 8.972 -8.458 1.00 0.00 PROA H
ATOM 224 N LED 14 1.949 1.677 -11.164 1.00 0.00 PROA N
ATOM 225 CA LED 14 2.871 0.550 -11.169 1.00 0.00 PROA C
ATOM 226 C LED 14 2.363 -0.544 -12.033 1.00 0.00 PROA C
ATOM 227 O LED 14 2.394 -0.492 -13.234 1.00 0.00 PROA O
ATOM 228 CB LED 14 4.233 0.971 -11.900 1.00 0.00 PROA C
ATOM 229 CG LED 14 5.224 1.863 -11.194 1.00 0.00 PROA C
ATOM 230 CD1 LED 14 5.247 1.597 -9.660 1.00 0.00 PROA C
ATOM 231 CD2 LED 14 6.616 1.678 -11.776 1.00 0.00 PROA C
ATOM 232 HN LED 14 1.585 2.080 -12.000 1.00 0.00 PROA H
ATOM 233 HA LED 14 3.044 0.061 -10.222 1.00 0.00 PROA H
ATOM 234 HB1 LED 14 4.785 0.024 -12.083 1.00 0.00 PROA H
ATOM 235 HB2 LED 14 4.028 1.506 -12.852 1.00 0.00 PROA H
ATOM 236 HG LED 14 4.958 2.930 -11.354 1.00 0.00 PROA H
ATOM 237 HD11 LED 14 5.878 2.261 -9.031 1.00 0.00 PROA H
ATOM 238 HD12 LED 14 4.244 1.688 -9.192 1.00 0.00 PROA H
ATOM 239 HD13 LED 14 5.537 0.559 -9.390 1.00 0.00 PROA H
ATOM 240 HD21 LED 14 7.437 2.057 -11.131 1.00 0.00 PROA H
ATOM 241 HD22 LED 14 6.864 1.962 -12.822 1.00 0.00 PROA H
ATOM 242 HD23 LED 14 6.805 0.583 -11.783 1.00 0.00 PROA H
ATOM 243 N TRP 15 1.930 -1.645 -11.408 1.00 0.00 PROA N
ATOM 244 CA TRP 15 1.418 -2.881 -11.998 1.00 0.00 PROA C
ATOM 245 C TRP 15 -0.080 -3.078 -11.632 1.00 0.00 PROA C
ATOM 246 O TRP 15 -0.586 -2.694 -10.554 1.00 0.00 PROA O
ATOM 247 CB TRP 15 2.248 -4.139 -11.454 1.00 0.00 PROA C
ATOM 248 CG TRP 15 3.640 -4.167 -11.948 1.00 0.00 PROA C
ATOM 249 CD1 TRP 15 4.150 -4.529 -13.167 1.00 0.00 PROA C
ATOM 250 CD2 TRP 15 4.718 -3.577 -11.214 1.00 0.00 PROA C
ATOM 251 CE2 TRP 15 5.914 -3.698 -12.003 1.00 0.00 PROA C
ATOM 252 CE3 TRP 15 4.862 -3.000 -9.953 1.00 0.00 PROA C
ATOM 253 NE1 TRP 15 5.473 -4.242 -13.228 1.00 0.00 PROA N
ATOM 254 CZ2 TRP 15 7.119 -3.135 -11.641 1.00 0.00 PROA C
ATOM 255 CZ3 TRP 15 6.101 -2.432 -9.632 1.00 0.00 PROA C
ATOM 256 CH2 TRP 15 7.211 -2.430 -10.485 1.00 0.00 PROA C
ATOM 257 HN TRP 15 1.949 -1.728 -10.415 1.00 0.00 PROA H
ATOM 258 HA TRP 15 1.500 -2.820 -13.073 1.00 0.00 PROA H
ATOM 259 HB1 TRP 15 2.174 -4.199 -10.347 1.00 0.00 PROA H
ATOM 260 HB2 TRP 15 1.674 -5.050 -11.728 1.00 0.00 PROA H
ATOM 261 HD1 TRP 15 3.558 -5.078 -13.884 1.00 0.00 PROA H
ATOM 262 HE1 TRP 15 6.131 -4.458 -13.916 1.00 0.00 PROA H
ATOM 263 HE3 TRP 15 4.006 -2.814 -9.320 1.00 0.00 PROA H
ATOM 264 HZ2 TRP 15 7.976 -3.068 -12.294 1.00 0.00 PROA H
ATOM 265 HZ3 TRP 15 6.258 -1.932 -8.688 1.00 0.00 PROA H
ATOM 266 HH2 TRP 15 8.174 -2.003 -10.246 1.00 0.00 PROA H
ATOM 267 N EAM 16 -0.804 -3.634 -12.520 1.00 0.00 PROA N
ATOM 268 CA EAM 16 -2.114 -4.149 -12.293 1.00 0.00 PROA C
ATOM 269 CB EAM 16 -2.380 -5.177 -13.378 1.00 0.00 PROA C
ATOM 270 OH1 EAM 16 -3.622 -5.794 -13.030 1.00 0.00 PROA O
ATOM 271 HN1 EAM 16 -0.343 -3.876 -13.370 1.00 0.00 PROA H
ATOM 272 HA1 EAM 16 -2.104 -4.679 -11.352 1.00 0.00 PROA H
ATOM 273 HA2 EAM 16 -2.774 -3.302 -12.399 1.00 0.00 PROA H
ATOM 274 HB1 EAM 16 -1.548 -5.903 -13.254 1.00 0.00 PROA H
ATOM 275 HB2 EAM 16 -2.423 -4.710 -14.385 1.00 0.00 PROA H
ATOM 276 HO1 EAM 16 -4.003 -6.001 -13.887 1.00 0.00 PROA H
TER 277 EAM 16
ATOM 278 C CHO 0 -2.524 3.274 0.271 1.00 0.00 PROB C
ATOM 279 O CHO 0 -2.366 3.583 1.443 1.00 0.00 PROB O
ATOM 280 HA CHO 0 -1.956 3.665 -0.586 1.00 0.00 PROB H
ATOM 281 N VAL 1 -3.523 2.406 -0.065 1.00 0.00 PROB N
ATOM 282 CA VAL 1 -4.182 1.651 0.939 1.00 0.00 PROB C
ATOM 283 C VAL 1 -4.063 0.148 0.606 1.00 0.00 PROB C
ATOM 284 O VAL 1 -4.276 -0.259 -0.502 1.00 0.00 PROB O
ATOM 285 CB VAL 1 -5.634 2.112 0.921 1.00 0.00 PROB C
ATOM 286 CG1 VAL 1 -6.629 1.196 1.726 1.00 0.00 PROB C
ATOM 287 CG2 VAL 1 -5.735 3.613 1.370 1.00 0.00 PROB C
ATOM 288 HN VAL 1 -3.569 2.130 -1.022 1.00 0.00 PROB H
ATOM 289 HA VAL 1 -3.689 1.796 1.889 1.00 0.00 PROB H
ATOM 290 HB VAL 1 -5.879 2.072 -0.162 1.00 0.00 PROB H
ATOM 291 HG11 VAL 1 -6.289 1.217 2.784 1.00 0.00 PROB H
ATOM 292 HG12 VAL 1 -7.690 1.509 1.625 1.00 0.00 PROB H
ATOM 293 HG13 VAL 1 -6.539 0.167 1.318 1.00 0.00 PROB H
ATOM 294 HG21 VAL 1 -5.372 3.744 2.412 1.00 0.00 PROB H
ATOM 295 HG22 VAL 1 -6.792 3.956 1.370 1.00 0.00 PROB H
ATOM 296 HG23 VAL 1 -5.148 4.250 0.675 1.00 0.00 PROB H
ATOM 297 N GLY 2 -3.601 -0.707 1.569 1.00 0.00 PROB N
ATOM 298 CA GLY 2 -3.545 -2.165 1.350 1.00 0.00 PROB C
ATOM 299 C GLY 2 -2.420 -2.728 2.095 1.00 0.00 PROB C
ATOM 300 O GLY 2 -2.060 -2.185 3.171 1.00 0.00 PROB O
ATOM 301 HN GLY 2 -3.269 -0.388 2.453 1.00 0.00 PROB H
ATOM 302 HA1 GLY 2 -3.496 -2.362 0.289 1.00 0.00 PROB H
ATOM 303 HA2 GLY 2 -4.502 -2.485 1.736 1.00 0.00 PROB H
ATOM 304 N ALA 3 -1.830 -3.869 1.644 1.00 0.00 PROB N
ATOM 305 CA ALA 3 -0.758 -4.570 2.301 1.00 0.00 PROB C
ATOM 306 C ALA 3 0.658 -4.158 1.930 1.00 0.00 PROB C
ATOM 307 O ALA 3 1.088 -4.394 0.812 1.00 0.00 PROB O
ATOM 308 CB ALA 3 -1.037 -6.087 2.251 1.00 0.00 PROB C
ATOM 309 HN ALA 3 -2.071 -4.191 0.731 1.00 0.00 PROB H
ATOM 310 HA ALA 3 -0.850 -4.211 3.316 1.00 0.00 PROB H
ATOM 311 HB1 ALA 3 -0.229 -6.595 2.819 1.00 0.00 PROB H
ATOM 312 HB2 ALA 3 -2.035 -6.360 2.656 1.00 0.00 PROB H
ATOM 313 HB3 ALA 3 -0.961 -6.501 1.223 1.00 0.00 PROB H
ATOM 314 N LED 4 1.436 -3.505 2.776 1.00 0.00 PROB N
ATOM 315 CA LED 4 2.820 -3.189 2.613 1.00 0.00 PROB C
ATOM 316 C LED 4 3.209 -2.036 3.655 1.00 0.00 PROB C
ATOM 317 O LED 4 3.460 -2.269 4.869 1.00 0.00 PROB O
ATOM 318 CB LED 4 3.793 -4.437 2.740 1.00 0.00 PROB C
ATOM 319 CG LED 4 5.245 -4.261 2.330 1.00 0.00 PROB C
ATOM 320 CD1 LED 4 5.351 -3.793 0.883 1.00 0.00 PROB C
ATOM 321 CD2 LED 4 6.193 -3.434 3.201 1.00 0.00 PROB C
ATOM 322 HN LED 4 1.111 -3.279 3.691 1.00 0.00 PROB H
ATOM 323 HA LED 4 2.879 -2.731 1.637 1.00 0.00 PROB H
ATOM 324 HB1 LED 4 3.619 -4.890 3.740 1.00 0.00 PROB H
ATOM 325 HB2 LED 4 3.341 -5.133 2.002 1.00 0.00 PROB H
ATOM 326 HG LED 4 5.791 -5.225 2.255 1.00 0.00 PROB H
ATOM 327 HD11 LED 4 6.388 -3.816 0.486 1.00 0.00 PROB H
ATOM 328 HD12 LED 4 4.735 -4.454 0.236 1.00 0.00 PROB H
ATOM 329 HD13 LED 4 5.035 -2.730 0.817 1.00 0.00 PROB H
ATOM 330 HD21 LED 4 7.196 -3.241 2.763 1.00 0.00 PROB H
ATOM 331 HD22 LED 4 6.248 -3.877 4.218 1.00 0.00 PROB H
ATOM 332 HD23 LED 4 5.821 -2.402 3.379 1.00 0.00 PROB H
ATOM 333 N ALA 5 3.276 -0.728 3.213 1.00 0.00 PROB N
ATOM 334 CA ALA 5 3.439 0.393 4.090 1.00 0.00 PROB C
ATOM 335 C ALA 5 2.604 1.580 3.571 1.00 0.00 PROB C
ATOM 336 O ALA 5 2.505 1.722 2.391 1.00 0.00 PROB O
ATOM 337 CB ALA 5 4.898 0.827 4.222 1.00 0.00 PROB C
ATOM 338 HN ALA 5 3.216 -0.547 2.235 1.00 0.00 PROB H
ATOM 339 HA ALA 5 3.070 0.206 5.088 1.00 0.00 PROB H
ATOM 340 HB1 ALA 5 5.094 1.481 5.099 1.00 0.00 PROB H
ATOM 341 HB2 ALA 5 5.473 -0.113 4.359 1.00 0.00 PROB H
ATOM 342 HB3 ALA 5 5.288 1.251 3.272 1.00 0.00 PROB H
ATOM 343 N VAD 6 2.058 2.443 4.421 1.00 0.00 PROB N
ATOM 344 CA VAD 6 0.957 3.340 3.999 1.00 0.00 PROB C
ATOM 345 C VAD 6 -0.082 3.209 4.959 1.00 0.00 PROB C
ATOM 346 O VAD 6 0.113 3.226 6.153 1.00 0.00 PROB O
ATOM 347 CB VAD 6 1.366 4.840 3.761 1.00 0.00 PROB C
ATOM 348 CG1 VAD 6 2.765 5.023 3.129 1.00 0.00 PROB C
ATOM 349 CG2 VAD 6 0.270 5.401 2.903 1.00 0.00 PROB C
ATOM 350 HN VAD 6 2.261 2.200 5.367 1.00 0.00 PROB H
ATOM 351 HA VAD 6 0.612 2.983 3.040 1.00 0.00 PROB H
ATOM 352 HB VAD 6 1.401 5.344 4.751 1.00 0.00 PROB H
ATOM 353 HG11 VAD 6 2.801 4.750 2.053 1.00 0.00 PROB H
ATOM 354 HG12 VAD 6 3.583 4.487 3.656 1.00 0.00 PROB H
ATOM 355 HG13 VAD 6 3.048 6.096 3.175 1.00 0.00 PROB H
ATOM 356 HG21 VAD 6 0.067 4.795 1.994 1.00 0.00 PROB H
ATOM 357 HG22 VAD 6 0.621 6.420 2.635 1.00 0.00 PROB H
ATOM 358 HG23 VAD 6 -0.712 5.425 3.423 1.00 0.00 PROB H
ATOM 359 N VAL 7 -1.260 2.908 4.505 1.00 0.00 PROB N
ATOM 360 CA VAL 7 -2.456 2.748 5.336 1.00 0.00 PROB C
ATOM 361 C VAL 7 -3.011 1.351 5.190 1.00 0.00 PROB C
ATOM 362 O VAL 7 -3.042 0.916 4.044 1.00 0.00 PROB O
ATOM 363 CB VAL 7 -3.560 3.818 5.052 1.00 0.00 PROB C
ATOM 364 CG1 VAL 7 -4.542 3.726 6.288 1.00 0.00 PROB C
ATOM 365 CG2 VAL 7 -3.057 5.286 4.994 1.00 0.00 PROB C
ATOM 366 HN VAL 7 -1.479 2.852 3.534 1.00 0.00 PROB H
ATOM 367 HA VAL 7 -2.159 2.802 6.373 1.00 0.00 PROB H
ATOM 368 HB VAL 7 -4.120 3.501 4.146 1.00 0.00 PROB H
ATOM 369 HG11 VAL 7 -3.929 3.575 7.202 1.00 0.00 PROB H
ATOM 370 HG12 VAL 7 -5.191 4.614 6.444 1.00 0.00 PROB H
ATOM 371 HG13 VAL 7 -5.257 2.900 6.086 1.00 0.00 PROB H
ATOM 372 HG21 VAL 7 -2.602 5.561 4.018 1.00 0.00 PROB H
ATOM 373 HG22 VAL 7 -2.401 5.554 5.850 1.00 0.00 PROB H
ATOM 374 HG23 VAL 7 -3.874 6.034 5.088 1.00 0.00 PROB H
ATOM 375 N VAD 8 -3.410 0.536 6.240 1.00 0.00 PROB N
ATOM 376 CA VAD 8 -3.841 -0.870 5.891 1.00 0.00 PROB C
ATOM 377 C VAD 8 -3.150 -1.900 6.825 1.00 0.00 PROB C
ATOM 378 O VAD 8 -3.217 -1.839 8.046 1.00 0.00 PROB O
ATOM 379 CB VAD 8 -5.305 -1.058 6.145 1.00 0.00 PROB C
ATOM 380 CG1 VAD 8 -6.127 -0.204 5.223 1.00 0.00 PROB C
ATOM 381 CG2 VAD 8 -5.688 -2.552 5.876 1.00 0.00 PROB C
ATOM 382 HN VAD 8 -3.546 0.840 7.180 1.00 0.00 PROB H
ATOM 383 HA VAD 8 -3.630 -1.172 4.876 1.00 0.00 PROB H
ATOM 384 HB VAD 8 -5.529 -0.804 7.203 1.00 0.00 PROB H
ATOM 385 HG11 VAD 8 -7.159 -0.537 4.982 1.00 0.00 PROB H
ATOM 386 HG12 VAD 8 -5.621 -0.087 4.241 1.00 0.00 PROB H
ATOM 387 HG13 VAD 8 -6.183 0.851 5.566 1.00 0.00 PROB H
ATOM 388 HG21 VAD 8 -5.053 -3.429 6.125 1.00 0.00 PROB H
ATOM 389 HG22 VAD 8 -5.874 -2.597 4.782 1.00 0.00 PROB H
ATOM 390 HG23 VAD 8 -6.700 -2.799 6.262 1.00 0.00 PROB H
ATOM 391 N TRP 9 -2.403 -2.784 6.146 1.00 0.00 PROB N
ATOM 392 CA TRP 9 -1.575 -3.736 6.800 1.00 0.00 PROB C
ATOM 393 C TRP 9 -0.070 -3.577 6.600 1.00 0.00 PROB C
ATOM 394 O TRP 9 0.381 -3.506 5.473 1.00 0.00 PROB O
ATOM 395 CB TRP 9 -2.034 -5.171 6.444 1.00 0.00 PROB C
ATOM 396 CG TRP 9 -1.489 -6.355 7.207 1.00 0.00 PROB C
ATOM 397 CD1 TRP 9 -1.864 -6.707 8.479 1.00 0.00 PROB C
ATOM 398 CD2 TRP 9 -0.264 -7.101 6.861 1.00 0.00 PROB C
ATOM 399 CE2 TRP 9 0.143 -7.859 7.997 1.00 0.00 PROB C
ATOM 400 CE3 TRP 9 0.538 -7.121 5.768 1.00 0.00 PROB C
ATOM 401 NE1 TRP 9 -0.901 -7.664 8.953 1.00 0.00 PROB N
ATOM 402 CZ2 TRP 9 1.241 -8.658 7.990 1.00 0.00 PROB C
ATOM 403 CZ3 TRP 9 1.828 -7.825 5.757 1.00 0.00 PROB C
ATOM 404 CH2 TRP 9 2.100 -8.588 6.879 1.00 0.00 PROB C
ATOM 405 HN TRP 9 -2.270 -2.690 5.162 1.00 0.00 PROB H
ATOM 406 HA TRP 9 -1.719 -3.627 7.865 1.00 0.00 PROB H
ATOM 407 HB1 TRP 9 -3.132 -5.137 6.614 1.00 0.00 PROB H
ATOM 408 HB2 TRP 9 -1.943 -5.368 5.354 1.00 0.00 PROB H
ATOM 409 HD1 TRP 9 -2.715 -6.334 9.030 1.00 0.00 PROB H
ATOM 410 HE1 TRP 9 -0.730 -7.836 9.899 1.00 0.00 PROB H
ATOM 411 HE3 TRP 9 0.234 -6.648 4.846 1.00 0.00 PROB H
ATOM 412 HZ2 TRP 9 1.581 -9.249 8.828 1.00 0.00 PROB H
ATOM 413 HZ3 TRP 9 2.329 -7.781 4.802 1.00 0.00 PROB H
ATOM 414 HH2 TRP 9 3.003 -9.179 6.924 1.00 0.00 PROB H
ATOM 415 N LED 10 0.731 -3.507 7.657 1.00 0.00 PROB N
ATOM 416 CA LED 10 2.186 -3.410 7.672 1.00 0.00 PROB C
ATOM 417 C LED 10 2.709 -2.245 8.466 1.00 0.00 PROB C
ATOM 418 O LED 10 2.624 -2.288 9.646 1.00 0.00 PROB O
ATOM 419 CB LED 10 2.788 -4.735 8.265 1.00 0.00 PROB C
ATOM 420 CG LED 10 4.372 -4.975 8.126 1.00 0.00 PROB C
ATOM 421 CD1 LED 10 4.548 -6.259 8.846 1.00 0.00 PROB C
ATOM 422 CD2 LED 10 4.901 -5.009 6.639 1.00 0.00 PROB C
ATOM 423 HN LED 10 0.425 -3.586 8.603 1.00 0.00 PROB H
ATOM 424 HA LED 10 2.626 -3.293 6.692 1.00 0.00 PROB H
ATOM 425 HB1 LED 10 2.627 -4.636 9.360 1.00 0.00 PROB H
ATOM 426 HB2 LED 10 2.241 -5.610 7.854 1.00 0.00 PROB H
ATOM 427 HG LED 10 4.961 -4.147 8.573 1.00 0.00 PROB H
ATOM 428 HD11 LED 10 5.628 -6.500 8.942 1.00 0.00 PROB H
ATOM 429 HD12 LED 10 4.226 -6.162 9.905 1.00 0.00 PROB H
ATOM 430 HD13 LED 10 3.988 -7.114 8.410 1.00 0.00 PROB H
ATOM 431 HD21 LED 10 4.355 -5.827 6.122 1.00 0.00 PROB H
ATOM 432 HD22 LED 10 5.986 -5.221 6.528 1.00 0.00 PROB H
ATOM 433 HD23 LED 10 4.693 -4.012 6.196 1.00 0.00 PROB H
ATOM 434 N TRP 11 3.256 -1.208 7.830 1.00 0.00 PROB N
ATOM 435 CA TRP 11 3.923 -0.070 8.485 1.00 0.00 PROB C
ATOM 436 C TRP 11 3.224 1.233 8.067 1.00 0.00 PROB C
ATOM 437 O TRP 11 2.840 1.417 6.911 1.00 0.00 PROB O
ATOM 438 CB TRP 11 5.381 -0.043 8.115 1.00 0.00 PROB C
ATOM 439 CG TRP 11 6.178 -1.087 8.763 1.00 0.00 PROB C
ATOM 440 CD1 TRP 11 6.251 -1.161 10.083 1.00 0.00 PROB C
ATOM 441 CD2 TRP 11 7.043 -2.040 8.172 1.00 0.00 PROB C
ATOM 442 CE2 TRP 11 7.557 -2.764 9.282 1.00 0.00 PROB C
ATOM 443 CE3 TRP 11 7.305 -2.426 6.855 1.00 0.00 PROB C
ATOM 444 NE1 TRP 11 7.068 -2.186 10.412 1.00 0.00 PROB N
ATOM 445 CZ2 TRP 11 8.343 -3.879 9.114 1.00 0.00 PROB C
ATOM 446 CZ3 TRP 11 8.124 -3.544 6.694 1.00 0.00 PROB C
ATOM 447 CH2 TRP 11 8.709 -4.165 7.811 1.00 0.00 PROB C
ATOM 448 HN TRP 11 3.185 -1.280 6.838 1.00 0.00 PROB H
ATOM 449 HA TRP 11 3.890 -0.123 9.563 1.00 0.00 PROB H
ATOM 450 HB1 TRP 11 5.447 -0.229 7.022 1.00 0.00 PROB H
ATOM 451 HB2 TRP 11 5.832 0.953 8.315 1.00 0.00 PROB H
ATOM 452 HD1 TRP 11 5.637 -0.624 10.790 1.00 0.00 PROB H
ATOM 453 HE1 TRP 11 7.411 -2.406 11.299 1.00 0.00 PROB H
ATOM 454 HE3 TRP 11 6.831 -1.955 6.007 1.00 0.00 PROB H
ATOM 455 HZ2 TRP 11 8.718 -4.428 9.965 1.00 0.00 PROB H
ATOM 456 HZ3 TRP 11 8.385 -3.916 5.714 1.00 0.00 PROB H
ATOM 457 HH2 TRP 11 9.528 -4.855 7.670 1.00 0.00 PROB H
ATOM 458 N LED 12 2.847 2.089 9.089 1.00 0.00 PROB N
ATOM 459 CA LED 12 2.028 3.242 9.021 1.00 0.00 PROB C
ATOM 460 C LED 12 0.848 3.011 9.944 1.00 0.00 PROB C
ATOM 461 O LED 12 0.917 2.709 11.127 1.00 0.00 PROB O
ATOM 462 CB LED 12 2.777 4.534 9.418 1.00 0.00 PROB C
ATOM 463 CG LED 12 4.197 4.715 8.802 1.00 0.00 PROB C
ATOM 464 CD1 LED 12 4.182 4.733 7.290 1.00 0.00 PROB C
ATOM 465 CD2 LED 12 4.803 5.987 9.328 1.00 0.00 PROB C
ATOM 466 HN LED 12 2.965 1.787 10.032 1.00 0.00 PROB H
ATOM 467 HA LED 12 1.665 3.439 8.023 1.00 0.00 PROB H
ATOM 468 HB1 LED 12 2.189 5.462 9.255 1.00 0.00 PROB H
ATOM 469 HB2 LED 12 3.004 4.468 10.504 1.00 0.00 PROB H
ATOM 470 HG LED 12 4.741 3.804 9.133 1.00 0.00 PROB H
ATOM 471 HD11 LED 12 4.209 3.714 6.848 1.00 0.00 PROB H
ATOM 472 HD12 LED 12 3.148 5.084 7.087 1.00 0.00 PROB H
ATOM 473 HD13 LED 12 5.019 5.395 6.981 1.00 0.00 PROB H
ATOM 474 HD21 LED 12 4.305 6.915 8.976 1.00 0.00 PROB H
ATOM 475 HD22 LED 12 4.951 5.998 10.429 1.00 0.00 PROB H
ATOM 476 HD23 LED 12 5.845 5.936 8.945 1.00 0.00 PROB H
ATOM 477 N TRP 13 -0.350 3.206 9.393 1.00 0.00 PROB N
ATOM 478 CA TRP 13 -1.600 3.293 10.105 1.00 0.00 PROB C
ATOM 479 C TRP 13 -2.538 2.158 9.831 1.00 0.00 PROB C
ATOM 480 O TRP 13 -2.753 1.768 8.620 1.00 0.00 PROB O
ATOM 481 CB TRP 13 -2.356 4.615 9.816 1.00 0.00 PROB C
ATOM 482 CG TRP 13 -1.722 5.889 10.267 1.00 0.00 PROB C
ATOM 483 CD1 TRP 13 -1.895 6.630 11.344 1.00 0.00 PROB C
ATOM 484 CD2 TRP 13 -0.728 6.619 9.429 1.00 0.00 PROB C
ATOM 485 CE2 TRP 13 -0.434 7.789 10.156 1.00 0.00 PROB C
ATOM 486 CE3 TRP 13 -0.073 6.414 8.205 1.00 0.00 PROB C
ATOM 487 NE1 TRP 13 -1.179 7.733 11.299 1.00 0.00 PROB N
ATOM 488 CZ2 TRP 13 0.406 8.731 9.702 1.00 0.00 PROB C
ATOM 489 CZ3 TRP 13 0.907 7.389 7.736 1.00 0.00 PROB C
ATOM 490 CH2 TRP 13 1.038 8.624 8.442 1.00 0.00 PROB C
ATOM 491 HN TRP 13 -0.427 3.356 8.410 1.00 0.00 PROB H
ATOM 492 HA TRP 13 -1.462 3.261 11.176 1.00 0.00 PROB H
ATOM 493 HB1 TRP 13 -2.565 4.734 8.731 1.00 0.00 PROB H
ATOM 494 HB2 TRP 13 -3.285 4.706 10.419 1.00 0.00 PROB H
ATOM 495 HD1 TRP 13 -2.629 6.368 12.092 1.00 0.00 PROB H
ATOM 496 HE1 TRP 13 -1.077 8.343 12.054 1.00 0.00 PROB H
ATOM 497 HE3 TRP 13 -0.270 5.552 7.585 1.00 0.00 PROB H
ATOM 498 HZ2 TRP 13 0.460 9.691 10.195 1.00 0.00 PROB H
ATOM 499 HZ3 TRP 13 1.384 7.127 6.804 1.00 0.00 PROB H
ATOM 500 HH2 TRP 13 1.763 9.368 8.146 1.00 0.00 PROB H
ATOM 501 N LED 14 -3.272 1.531 10.838 1.00 0.00 PROB N
ATOM 502 CA LED 14 -4.191 0.410 10.712 1.00 0.00 PROB C
ATOM 503 C LED 14 -3.763 -0.845 11.589 1.00 0.01 PROB C
ATOM 504 O LED 14 -3.692 -0.803 12.821 1.00 0.04 PROB O
ATOM 505 CB LED 14 -5.634 0.802 11.254 1.00 0.01 PROB C
ATOM 506 CG LED 14 -6.293 1.920 10.406 1.00 0.00 PROB C
ATOM 507 CD1 LED 14 -6.714 1.361 9.072 1.00 0.00 PROB C
ATOM 508 CD2 LED 14 -7.511 2.560 11.125 1.00 0.00 PROB C
ATOM 509 HN LED 14 -3.386 2.020 11.699 1.00 0.00 PROB H
ATOM 510 HA LED 14 -4.274 0.138 9.670 1.00 0.00 PROB H
ATOM 511 HB1 LED 14 -6.313 -0.070 11.363 1.00 0.00 PROB H
ATOM 512 HB2 LED 14 -5.552 1.148 12.307 1.00 0.00 PROB H
ATOM 513 HG LED 14 -5.572 2.761 10.317 1.00 0.00 PROB H
ATOM 514 HD11 LED 14 -6.906 2.235 8.413 1.00 0.00 PROB H
ATOM 515 HD12 LED 14 -5.898 0.807 8.561 1.00 0.00 PROB H
ATOM 516 HD13 LED 14 -7.574 0.659 9.119 1.00 0.00 PROB H
ATOM 517 HD21 LED 14 -8.278 1.763 11.228 1.00 0.02 PROB H
ATOM 518 HD22 LED 14 -7.810 3.374 10.431 1.00 0.00 PROB H
ATOM 519 HD23 LED 14 -7.397 3.089 12.095 1.00 0.00 PROB H
ATOM 520 N TRP 15 -3.320 -1.903 10.873 1.00 0.00 PROB N
ATOM 521 CA TRP 15 -2.986 -3.110 11.434 1.00 0.01 PROB C
ATOM 522 C TRP 15 -1.628 -3.584 10.947 1.00 0.00 PROB C
ATOM 523 O TRP 15 -0.954 -3.076 10.041 1.00 0.00 PROB O
ATOM 524 CB TRP 15 -3.930 -4.266 10.988 1.00 0.01 PROB C
ATOM 525 CG TRP 15 -5.308 -4.170 11.564 1.00 0.02 PROB C
ATOM 526 CD1 TRP 15 -5.743 -4.670 12.800 1.00 0.05 PROB C
ATOM 527 CD2 TRP 15 -6.462 -3.526 11.017 1.00 0.00 PROB C
ATOM 528 CE2 TRP 15 -7.564 -3.693 11.968 1.00 0.03 PROB C
ATOM 529 CE3 TRP 15 -6.653 -2.713 9.884 1.00 0.00 PROB C
ATOM 530 NE1 TRP 15 -7.118 -4.466 12.994 1.00 0.05 PROB N
ATOM 531 CZ2 TRP 15 -8.858 -3.199 11.713 1.00 0.03 PROB C
ATOM 532 CZ3 TRP 15 -7.948 -2.198 9.720 1.00 0.00 PROB C
ATOM 533 CH2 TRP 15 -9.038 -2.456 10.539 1.00 0.00 PROB C
ATOM 534 HN TRP 15 -3.156 -1.831 9.892 1.00 0.00 PROB H
ATOM 535 HA TRP 15 -2.972 -3.106 12.514 1.00 0.03 PROB H
ATOM 536 HB1 TRP 15 -3.970 -4.432 9.890 1.00 0.00 PROB H
ATOM 537 HB2 TRP 15 -3.607 -5.293 11.263 1.00 0.00 PROB H
ATOM 538 HD1 TRP 15 -5.148 -5.244 13.495 1.00 0.06 PROB H
ATOM 539 HE1 TRP 15 -7.781 -4.981 13.491 1.00 0.10 PROB H
ATOM 540 HE3 TRP 15 -5.842 -2.452 9.220 1.00 0.00 PROB H
ATOM 541 HZ2 TRP 15 -9.727 -3.355 12.335 1.00 0.05 PROB H
ATOM 542 HZ3 TRP 15 -8.080 -1.603 8.829 1.00 0.00 PROB H
ATOM 543 HH2 TRP 15 -10.021 -2.041 10.373 1.00 0.00 PROB H
ATOM 544 N EAM 16 -0.994 -4.612 11.586 1.00 0.00 PROB N
ATOM 545 CA EAM 16 0.185 -5.098 11.055 1.00 0.00 PROB C
ATOM 546 CB EAM 16 0.697 -6.182 12.111 1.00 0.00 PROB C
ATOM 547 OH1 EAM 16 -0.099 -7.360 12.098 1.00 0.00 PROB O
ATOM 548 HN1 EAM 16 -1.278 -4.907 12.496 1.00 0.00 PROB H
ATOM 549 HA1 EAM 16 0.038 -5.430 10.038 1.00 0.00 PROB H
ATOM 550 HA2 EAM 16 0.879 -4.274 11.140 1.00 0.00 PROB H
ATOM 551 HB1 EAM 16 0.682 -5.745 13.133 1.00 0.00 PROB H
ATOM 552 HB2 EAM 16 1.685 -6.590 11.808 1.00 0.02 PROB H
ATOM 553 HO1 EAM 16 0.324 -7.926 12.748 1.00 0.00 PROB H
END
Raw
helix.py
import numpy as np
from pymol import cmd
from pymol.cgo import *
from math import *
from pymol import stored
# helix vector
stored.backbone = []
stored.name = []
cmd.iterate_state(1, selector.process("( name ca )"), "stored.backbone.append([x,y,z])")
cmd.iterate_state(1, selector.process("( name ca )"), "stored.name.append(name)")
natom = len(stored.backbone)
com = np.sum(stored.backbone, axis=0) / float(natom)
def r(v): return math.sqrt(v[0]**2 + v[1]**2 + v[2]**2)
def dist(a, b): return r((a[0]-b[0], a[1]-b[1], a[2]-b[2]))
def mass(name):
m = {'N': 14, 'C': 12, 'O': 16}
return m[name[0]]
def moi(i, j, sel, ref):
"""
Generalized moment of inertia element--both diagonal and off
diagonal. Coordinate axes i and j should be 'x', 'y', or 'z'.
The sel argument is a list of Atoms.
The ref arguemnt is a Point.
"""
kd = lambda x,y: x==y
def getattr(o, i):
m = {'x': 0, 'y': 1, 'z': 2}
return o[m[i]]
delta = kd(i, j)
refi = getattr(ref, i)
refj = getattr(ref, j)
el = []
index = 0
for atom in sel:
m = mass(stored.name[index])
r2d = (dist(atom, ref)**2) * delta
ri = getattr(atom, i) - refi
rj = getattr(atom, j) - refj
el.append(m*(r2d - ri*rj))
index += 1
return sum(el)
indices = [(i,j) for i in 'xyz' for j in 'xyz']
tensor = np.reshape(np.array([moi(i,j,stored.backbone,com) for (i,j) in indices]), (3,3))
w, v = np.linalg.eig(tensor)
print w, v
from arrow import *
a1 = [-v[0][0], -v[1][0], -v[2][0]]
a2 = [v[0][1], v[1][1], v[2][1]]
a3 = [v[0][2], v[1][2], v[2][2]]
l = 16
cmd.delete('junk')
cgo_arrow((com[0]-l*a1[0], com[1]-l*a1[1], com[2]-l*a1[2]), (com[0]+l*a1[0], com[1]+l*a1[1], com[2]+l*a1[2]), name='junk')
# draw cylinder
obj = [ 25.0, 0.4,
CYLINDER, com[0]-l*a1[0], com[1]-l*a1[1], com[2]-l*a1[2], com[0]+l*a1[0], com[1]+l*a1[1], com[2]+l*a1[2], 3.5, 0.48, 0.78, 0.48, 0.48, 0.78, 0.48,
COLOR, 0.56, 1.0, 0.56,
BEGIN, END ]
cmd.load_cgo( obj, 'junk99', 1 )
# reference vector
stored.ref = []
cmd.iterate_state(1, selector.process("resi 9 and ( name ca ) and segid proa"), "stored.ref.append([x,y,z])")
ref = [stored.ref[0][0], stored.ref[0][1], stored.ref[0][2]]
r = [com[0]-ref[0], com[1]-ref[1], com[2]-ref[2]]
t = np.dot(r, a1) / np.dot(a1, a1)
h = [com[0] - a1[0]*t, com[1] - a1[1]*t, com[2] - a1[2]*t]
ref = [ref[i]+(ref[i]-h[i])*3 for i in range(3)]
cmd.delete('junk2')
cgo_arrow((h[0], h[1], h[2]), (ref[0], ref[1], ref[2]), name='junk2')
# cross vector
c = np.cross(a1, [ref[i]-h[i] for i in range(3)])
cmd.delete('junk3')
cgo_arrow((h[0], h[1], h[2]), [-c[i]+h[i] for i in range(3)], name='junk3')
# Z-axis
cmd.delete('junk4')
cgo_arrow((h[0], h[1], h[2]), (-6, -6, 10), name='junk4')
# plane
def _plane(corner1, corner2, corner3, corner4, normal):
planeObj = []
planeObj.extend([ALPHA, 0.6])
planeObj.extend([COLOR, 0.8, 0.8, 0.8])
planeObj.extend([BEGIN, TRIANGLE_STRIP])
planeObj.append(NORMAL)
planeObj.extend(normal)
for corner in [corner1, corner2, corner3, corner4, corner1]:
planeObj.append(VERTEX)
planeObj.extend(corner)
planeObj.extend([ALPHA, 0])
planeObj.append(END)
return planeObj
def makePrimitive(cgo, name):
cmd.set('auto_zoom', 0, quiet=1)
cmd.load_cgo(cgo, name)
cmd.set('auto_zoom', 1, quiet=1)
cmd.delete('junk5')
plane = _plane(ref, h, [-c[i]+h[i] for i in range(3)], [ref[i]+h[i]-c[i]-h[i] for i in range(3)], a1)
makePrimitive(plane, 'junk5')
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment