X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fpymol%2Fshow_UNRES.py;h=e922779ca98bc0f26c7ee0a302e9c50ce72c18e1;hb=0ea7c642634cc4072d680200667850960ea0c820;hp=673a269e8e18d87842ab6f032ef0855da03df092;hpb=9b1dc261d85743c07a1c71414505ae883bce1648;p=unres.git

diff --git a/source/pymol/show_UNRES.py b/source/pymol/show_UNRES.py
index 673a269..e922779 100644
--- a/source/pymol/show_UNRES.py
+++ b/source/pymol/show_UNRES.py
@@ -27,7 +27,7 @@ def show_UNRES(sl='(all)'):
 	p_radius = 0.6
 	e_size = 1.0
 	# residue dictionary
-	# resn = [color_Red, color_Green, color_Blue, elipsoid_side_width ]
+	# resn = [color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
 	resdb = {	'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
 				'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
 				'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
@@ -54,17 +54,17 @@ def show_UNRES(sl='(all)'):
 	# Get pseudo-peptide group positions
 	atoms=cmd.get_model(sl+" & n. CA").atom
 	p=[]
-	for i in range(0,len(atoms)-1):
+	for i in xrange(0,len(atoms)-1):
 		p.append( [atoms[i].coord[0]+(atoms[i+1].coord[0]-atoms[i].coord[0])/2, atoms[i].coord[1]+(atoms[i+1].coord[1]-atoms[i].coord[1])/2, atoms[i].coord[2]+(atoms[i+1].coord[2]-atoms[i].coord[2])/2 ] )
 	obj=[]
-	for i in range(0,len(p)):
+	for i in xrange(0,len(p)):
 		obj.extend( [ COLOR, 0.643, 0.933, 0.960 ] )
 		obj.extend( [ SPHERE, p[i][0], p[i][1], p[i][2], p_radius ] )
 
 	# Get Sidechain elipsoids positions
 	atoms=cmd.get_model(sl+" & n. CB").atom
 	e=[]
-	for i in range(0,len(atoms)):
+	for i in xrange(0,len(atoms)):
 		ca=cmd.get_model(sl+" & n. CA & resn "+atoms[i].resn+" & resi "+atoms[i].resi).atom
 		e.append( [ atoms[i].resn, atoms[i].coord[0], atoms[i].coord[1], atoms[i].coord[2], atoms[i].coord[0]-ca[0].coord[0], atoms[i].coord[1]-ca[0].coord[1], atoms[i].coord[2]-ca[0].coord[2] ] )
 
@@ -73,29 +73,39 @@ def show_UNRES(sl='(all)'):
     #
 	# [ ELLIPSOID, x_pos, y_pos, z_pos, size, x0, y0, z0, x1, y1, z2, x2, y2, z2 ]
 	# where the xyz vectors are orthogonal and of length 1.0 or less.
-	for i in range(0,len(e)):
+	for i in xrange(0,len(e)):
 		# vactor CB->CA
 		tmp0=[e[i][4], e[i][5], e[i][6]]
-		l=cpv.length(tmp0)
+		#l=cpv.length(tmp0)
 		# random vector
 		tmp1 = cpv.random_vector()
 		# orthogonal vector to tmp0 and tmp1 
 		tmp2 = cpv.cross_product(tmp1, tmp0)
 		tmp3 = cpv.cross_product(tmp0, tmp2)
+		tmp0 = cpv.normalize(tmp0)
 		tmp2 = cpv.normalize(tmp2)
 		tmp3 = cpv.normalize(tmp3)
+		tmp0 = cpv.scale(tmp0,resdb[e[i][0]][4])
 		tmp2 = cpv.scale(tmp2,resdb[e[i][0]][3])
 		tmp3 = cpv.scale(tmp3,resdb[e[i][0]][3])
 		factor = 1.0 / max( cpv.length(tmp0), cpv.length(tmp2), cpv.length(tmp3))
 		tmp0 = cpv.scale(tmp0, factor)
 		tmp2 = cpv.scale(tmp2, factor)
 		tmp3 = cpv.scale(tmp3, factor)
-		
-		#print factor, cpv.length(tmp0), cpv.length(tmp2), cpv.length(tmp3)			
 		obj.extend( [ COLOR, resdb[e[i][0]][0], resdb[e[i][0]][1], resdb[e[i][0]][2] ] )
-		#obj.extend( [ NORMAL, 1, 0, 0 ] )
 		obj.extend( [ ELLIPSOID, e[i][1], e[i][2], e[i][3], 1.0/factor, ] + tmp0 + tmp2 + tmp3 )
 
+	# Get Glicynes positions
+	atoms=cmd.get_model(sl+' & n. CA & resn GLY').atom
+	g=[]
+	for i in xrange(0,len(atoms)):
+		g.append( [ atoms[i].resn, atoms[i].coord[0], atoms[i].coord[1], atoms[i].coord[2] ])
+	# Draw the glicyne spheres	
+	for i in xrange(0, len(g)):
+		obj.extend( [ COLOR, resdb[g[i][0]][0], resdb[g[i][0]][1], resdb[g[i][0]][2] ] )
+		obj.extend( [ SPHERE, g[i][1], g[i][2], g[i][3], resdb[g[i][0]][3]])
+
+
 	cmd.set('cgo_ellipsoid_quality', 2)
 	cmd.load_cgo(obj,'UNRES_'+sl)