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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