From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Thu Mar 15 2007 - 21:16:26 CDT

I asked about using VMD to overlay two structures using several atoms
in each molecule. I got a very nice reply from Mikolai Fajer. I
really appreciated it. I got it to work at the time. However, I'm
trying to use it now and I'm getting odd errors.

I select 4 atoms on each molecule using: set base_original [atomselect
0 "index 2645 to 2648"] and set base_new [atomselect 1 "index 2 to 5"]

I used set matrix [measure fit $base_new $base_original]

and keep getting told: measure fit: selections must have the same
number of atoms

I tried to select the atoms one at a time "index 2 3 4 5" etc and get
the same error.

They do. I'm not sure what the problem is. Does anyone have any
questions?

Thanks

Kara Di Giorgio

p.s. I'm adding the tkconsole info from my attempt:

loading history file ... 48 events added
Main console display active (Tcl8.4.2 / Tk8.4.2)
(research) 49 % set base_original [atomselect 0 "index 2645-2648"]
atomselect: cannot parse selection text: index 2645-2648
>Main< (research) 50 % set base_original [atomselect 0 "index 2645 to
2648"]
atomselect0
>Main< (research) 51 % set base_new [atomselect 1 "index 2 to 5"]
atomselect1
>Main< (research) 52 % set matrix [measure fit $base_new $base_original]
measure fit: selections must have the same number of atoms
>Main< (research) 53 % set base_ala [atomselect 0 "index 2645 2646 2647
2648"]
atomselect2
>Main< (research) 54 % set base_pca [atomselect 1 "index 2 3 4 5"]
atomselect3
>Main< (research) 55 % set matrix [measure fit $base_ala $base_pca]
measure fit: selections must have the same number of atoms
>Main< (research) 56 %