VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 20 2014 - 06:48:35 CST

On Mon, Jan 20, 2014 at 6:43 AM, <manali_at_bioinfo.net.in> wrote:
> Hi,
>
> I am trying to cluster a trajectory using several residues as a selection.
>
> set sel [atomselect top "protein and resid 771 772 775 779 782 785 805 806
> 807"]
>
> When i plot rmsd of this selection over time i get values from 1.2 to 2.7
> angstrom.
>
> I use the following command for clustering:
> measure cluster $sel distfunc fitrmsd cutoff 2
> & i get 2 clusters
> 0 1 2 3 4 {5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
> 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52
> 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77
> 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100}
> When i do
> measure cluster $sel distfunc fitrmsd cutoff 1
> i get the same exact result.
>
> What am i doing wrong? Thanks in advance for the pointers.

your mistake is probably that you didn't fully understand what measure
cluster does.

axel.

> -Manali
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.