Create a copy of the original chain, modify the chain, and fit the copy to the original.  For example
# PyMOL 1.2 .pml input
fab AAAAAAA, orig
create copy, orig
set_dihedral orig///3/C, orig///4/N, orig///4/CA, orig///4/C, 180
fit orig////CA, copy////CA

From: Vivek Ranjan []
Sent: Mon 8/17/2009 1:44 PM
Subject: [PyMOL] coordinate transformation


I am trying to modify dihedral angles of a polymer chain. Once I
perform all the required steps, I am able to orient the chain and
align the chain along the same axis as the original chain. But
unfortunately, pymol moves the chain to a different position.
Basically, it changes the coordinates in a way that the center of the
chain is at the origin. I want the chain to lie along the original
chain with backbones coinciding with each other (almost). Is that
possible in pymol ?

Thank you and Regards,

Vivek Ranjan

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