X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fpymol%2Fshow_UNRES.py;h=e922779ca98bc0f26c7ee0a302e9c50ce72c18e1;hb=34d3ad3987785642be58fb2f26557d3314215577;hp=a6097a43c8677363e2ee01472b1a33385adeff41;hpb=f690e8b70bab14132839afebf080d4a28363b226;p=unres.git

diff --git a/source/pymol/show_UNRES.py b/source/pymol/show_UNRES.py
index a6097a4..e922779 100644
--- a/source/pymol/show_UNRES.py
+++ b/source/pymol/show_UNRES.py
@@ -27,67 +27,84 @@ 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 ]
-	resdb = {	'CYS': [1.000, 1.000, 0.000, 2.96868],
-				'MET': [0.000, 1.000, 0.000, 3.08863],
-				'PHE': [0.000, 0.392, 0.000, 3.04238],
-				'ILE': [0.000, 1.000, 0.000, 3.17389],
-				'LEU': [0.000, 1.000, 0.000, 2.52078],
-				'VAL': [0.000, 1.000, 0.000, 2.68924],
-				'TRP': [0.000, 0.392, 0.000, 3.47403],
-				'TYR': [0.596, 0.984, 0.596, 3.35434],
-				'ALA': [0.000, 1.000, 0.000, 1.72686],
-				'GLY': [1.000, 1.000, 1.000, 1.11383],
-				'THR': [1.000, 0.000, 1.000, 2.59210],
-				'SER': [1.000, 0.000, 1.000, 1.68800],
-				'GLN': [1.000, 0.000, 1.000, 2.22201],
-				'ASN': [1.000, 0.000, 1.000, 2.24946],
-				'GLU': [1.000, 0.000, 0.000, 2.05551],
-				'ASP': [1.000, 0.000, 0.000, 1.77556],
-				'HIS': [1.000, 0.000, 1.000, 3.02627],
-				'ARG': [0.000, 0.000, 1.000, 3.25143],
-				'LYS': [0.000, 0.000, 1.000, 4.50054],
-				'PRO': [0.000, 1.000, 1.000, 2.20525]
+	# 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],
+				'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
+				'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
+				'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
+				'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
+				'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
+				'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
+				'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
+				'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
+				'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
+				'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
+				'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
+				'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
+				'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
+				'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
+				'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
+				'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
+				'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
 			}
 
 
 	# 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] ] )
 
+	obj.extend([NORMAL,  0.0,  1.0,  0.0])
 	# This is from pymol devel example cgo07.py form http://pymol.sourcearchive.com/documentation/1.2r1/cgo07_8py-source.html
     #
 	# [ 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)
-		tmp2 = cpv.scale(tmp2,0.9*resdb[e[i][0]][3])
-		tmp3 = cpv.scale(tmp3,0.9*resdb[e[i][0]][3])
-				
+		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)
 		obj.extend( [ COLOR, resdb[e[i][0]][0], resdb[e[i][0]][1], resdb[e[i][0]][2] ] )
-		obj.extend( [ ELLIPSOID, e[i][1], e[i][2], e[i][3], e_size, ] + tmp0 + tmp2 + tmp3 )
+		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)