Hi Kayva, You need to realize that the negative of a plane normal is also normal to the same plane — it just points in the opposite direction. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 7, 2016, at 12:28 PM, Kavya Shankar <kavshank@umail.iu.edu> wrote:
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
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