Hi Martin, You may also be interested in this script which you can use to draw an arrow from point A to point B:
cgo_arrow( start, end, radius, head_radius, head_length, name, state ) start = [ x1, y1, z1 ], end = [ x2, y2, z2 ] For lots of arrows you can use: cgo_arrows( X, radius, head_radius, head_length, name, state ) where X is a array: [ [ x11, y11, z11, x12, y12, z12 ], [ x21, y21, z21, x22, y22, z22 ], ... ] I hope it will be of some use. If you encounter any problems with these functions, please let me know. Also, if you use the script and have some nice results, I'd be interested to see that. Finally, if you have any suggestions for modification or addition, please also let me know. Best, Tsjerk On 11/2/06, DeLano Scientific <del...@delsci.info> wrote:
Martin, The PyOpenGL included with PyMOL is probably out of date. It hasn't seen much use since it cannot interface with PyMOL's built-in ray tracer. In contrast, CGO primitives can be ray traced, but as noted, CGOs are limited to lines, spheres, cylinders, and triangles. Cheers, DeLano Scientific LLC Email Support Services > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Martin Hofling > Sent: Wednesday, November 01, 2006 9:49 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] cones in pymol? > > Hello everybody, > > i found some cone related stuff in pyopengl (in contrib dir > of pymol). Is it usable from pymol in some way? It would be > great to visualize vector-fields with 3d-Arrows but you need > a cone and a cylinder to construct them. > Probably the performance when setting up through triangles is > or it looks really bad if they're to few triangles. > > Cheers > Martin > -- > Tipp- und Rechtschreibfehler sind absichtlich eingebaut und > dienen der Belustigung des Lesers :-) > > -------------------------------------------------------------- > ----------- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier Download IBM WebSphere Application Server > v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; > dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
-- Tsjerk A. Wassenaar, Ph.D. post-doc NMR, 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): 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 )
