Vivek,
 
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
 
unpick
 
fit orig////CA, copy////CA
 
Cheers,
Warren
 

From: Vivek Ranjan [mailto:vranjan@gmail.com]
Sent: Mon 8/17/2009 1:44 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] coordinate transformation

Hello,

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

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net