Hi, I have to find the normal of the protein and I am writing a python script that can do this. But when I run it, the normal is different. On chimera, I select *chain A* and *chain B* to get the plane. import chimera import os from cStringIO import StringIO from StructMeasure import centroid from StructMeasure import plane from chimera import numpyArrayFromAtoms for filename in os.listdir("test_python1"): print filename model1 = chimera.openModels.open('test_python1/'+filename) mol1 = model1[0] p = plane(numpyArrayFromAtoms(mol1.atoms)) print p.normal axis = chimera.Vector(p.normal) angle = 120 xf = chimera.Xform.rotation(axis,angle) #matrix = chimera.Xform.getOpenGLMatrix(xf) mol1.openState.localXform(xf) mem =StringIO() chimera.pdbWrite(model1,chimera.Xform.identity(),mem) words=filename.split('_') with open('test_python1/'+words[0]+'_2.pdb','w') as f: f.write(mem.getvalue()) Can you tell me where I am going wrong? For some proteins, it gives me the right plane and for others its different. Ex: 1l9q_1.pdb Opening 1l9q_1.pdb... #3, chain A: Cu-NIR #3, chain B: Cu-NIR #3, chain C: Cu-NIR 0.98101 0.0805021 0.176463 and Model #0 is 1l9q.pdb Distance information Angles/Torsions Axes axis name, length, center, direction Planes plane name, center, normal, radius plane: ( 19.690, 39.732, 48.459) (-0.981, -0.081, -0.176) 46.305 Centroids centroid name, center centroid: ( 19.690, 39.732, 48.459) Thanks. Regards, Kavya Shankar