From: manali_at_bioinfo.net.in
Date: Mon Jan 20 2014 - 05:43:39 CST

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.

-Manali