Hi William,
Maybe the attached python script will be of some use. It contains a
function (and some helper functions) to draw a CGO arrow in PyMOL. It
contains code for drawing a cone for the head of the arrow.
Hope it helps,
Tsjerk
On 1/10/07, William Scott wgsc...@chemistry.ucsc.edu wrote:
Let's ask on the pymol mailing list...
On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote:
Damn, I can convert my 1969 CNS base pair restraints into what they
call
CGO drawn lines, and thereby display enforced hydrogen bonds, but I
wish
to draw cones for the base pair ladder as ribbons can do it. Oh
well, ..
On Wed, 10 Jan 2007, William Scott wrote:
I think it is possible, but I don't know how.
On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote:
Hi Bill, is it possible to draw a cone-shape in pymol?
-
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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):
