[chimera-dev] (no subject)

[Kavya Shankar]

Sorry, I choose chain A,B and C to get the plane on chimera.

On Mon, Nov 7, 2016 at 3:28 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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