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
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
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,