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: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,

 

Cheers,

 

Martin