From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 20 2014 - 09:18:45 CST

please always copy the mailing list on your responses. thanks.

On Mon, Jan 20, 2014 at 9:55 AM, <manali_at_bioinfo.net.in> wrote:
> Can you help explain?

not without you first explaining how you understood the existing
explanation in the VMD user's guide.

axel.

>
>
>> 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.
>>
>
>
> --
> Manali Joshi,Ph.D.
> Assistant Professor, Bioinformatics Center,
> University of Pune, India
>
>

-- 
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.