[chimera-dev] plane normals

[Eric Pettersen]

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 at 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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