By providing the molecule’s own transform as the second argument, you are having pdbWrite output the model’s coordinates relative to it’s own transformation — essentially undoing any rotations or translations that have been applied to the model. You want to provide the identity matrix as the second argument, e.g. “chimera.Xform.identity()”.

Eric Pettersen

UCSF Computer Graphics Lab

On Oct 25, 2016, at 1:45 PM, Kavya Shankar <kavshank@umail.iu.edu> wrote:

Hi,

I am new to chimera and I am attempting to write a python script that would rotate the models by some angle and then writing it to another pdb file with changed coordinates.

import chimera
import os
from cStringIO import StringIO

for filename in os.listdir("test_python"):
print filename
model = chimera.openModels.open('test_python/'+filename)
mol = model[0]
axis = chimera.Vector(1,1,1)
angle = 180
xf = chimera.Xform.rotation(axis,angle)
matrix = chimera.Xform.getOpenGLMatrix(xf)
print mol.openState.xform
mol.openState.localXform(xf)
print mol.openState.xform

mem =StringIO()
chimera.pdbWrite(model,mol.openState.xform,mem)
print mol.openState.xform
with open('converted.pdb','w') as f:
f.write(mem.getvalue())

This is my code so far. When I run it, the converted.pdb file does not contain any changed coordinates. The coordinates of the atoms are same as before.

Am I making some mistake? Is there any other way of doing this easily?

Thanks.

Regards,
Kavya Shankar
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