Hi Martin,
I do this quite often in Pymol using the pair fit menu pull down.
Wizard > Pair_fitting
You can just click on the three atom pairs you need then "fit 3 pairs". You can
highlight the residues in question as stick to make it easier.
I'm sure you can use command line too
Pair_fit 1xyz//a/tyr61/cb, 1abc//a/tyr61/cb, 1xyz//a/tyr61/ca,
1abc//a/tyr61/ca, 1xyz//a/tyr61/c, 1abc//a/tyr61/c
Or something along those lines.
Hope this helps
Joel
_________________________________
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
From: Martin Breugst [mailto:mbreu...@ucla.edu]
Sent: Friday, 13 April 2012 5:34 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] How to overlay different structures?
Dear PyMOL users:
I want to use PyMOL to generate a nice figure showing six different transition
state structures superimposed in one single picture. I have already tried to
use the commands pair_fit, overlay, and align but I did not get the results I
have expected. Is there any way to tell PyMOL to overlay three atoms of each
structure (in order to define a uniform plane) and if there is, what specific
command do I have to use?
Thank you very much for your help and suggestions,
Cheers,
Martin
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