VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon Aug 27 2007 - 11:07:47 CDT

On Mon, Aug 27, 2007 at 09:58:31AM -0600, Jim Pfaendtner wrote:
> Leonardo,
>
> Thanks for the help and pointing me to that post. I tried exactly
> what you suggested in the previous post but I am getting a strange
> error. Here is my VMD output. I tried setting the "order" list both
> from $sel2 and $sel1 and I also did the fit before re-ordering just
> to make sure that worked too.
>
> Thank you!
> Jim
>
>
> % set sel1 [atomselect 0 "index 1 2 3 4"]
> atomselect0
> % set sel2 [atomselect 0 "index 5 6 7 8"]
> atomselect1
> % measure fit $sel1 $sel2
> {-0.707626342773 -0.53004014492 -0.467249810696 -117.393280029}
> {0.621917784214 -0.78109151125 -0.0558064132929 56.5098266602}
> {-0.335385233164 -0.330081045628 0.882362306118 -19.8030891418} {0.0
> 0.0 0.0 1.0}
> % measure fit $sel1 $sel2 order {8 7 6 5}
> measure fit: order parameter contains out-of-range atom index
> % measure fit $sel1 $sel2 order {4 3 2 1}
> measure fit: order parameter contains out-of-range atom index

The order is a 0-based list that rearranges the order of the list of
indices present in $sel2. This means that your command should read:

measure fit $sel1 $sel2 {3 2 1 0}

i.e., consider the elements of the list {5 6 7 8} in the order 3rd, 2nd,
1st, and 0th. Makes sense?

Best,
Leo 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign