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 Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand  

Skype: jtyndall

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From: Martin Breugst [mailto:mbreugst@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,