VMD-L Mailing List

From: Toni Giorgino (toni.giorgino_at_gmail.com)
Date: Fri Dec 10 2010 - 09:05:01 CST

Hi,

you could perhaps set a property, like beta=1, on the common residues; then
use "beta 1" as the selection in the RMSD trajectory tool.

Toni

2010/12/1 Antonija Tomić <piculast_at_gmail.com>

> Dear VMD Users,
>
>
> I have two different protein structures, belonging to two different
> enzymes. The only common thing they have is the coordination of the central
> zinc ion,; made by two histidines and one glutamate. I am trying to align
> these two structures according to this two histidines and the central zinc
> ion.
>
>
> I'm not sure how to overlap these two structures according to these three
> residues which have different resid in each structure.
>
>
> Can you help me with this?
>
>
> Thank you for your help in advance,
> Antonija
> 

-- 
Toni Giorgino, PhD - toni.giorgino_at_gmail.com - fax +39 0382 1850209
Post-doctoral research fellow - Universitat Pompeu Fabra
Computational Biochemistry and Biophysics Lab
Barcelona Biomedical Research Park (PRBB)
C/ Doctor Aiguader 88, 08003 Barcelona, Spain