VMD-L Mailing List

From: manali_at_bioinfo.net.in
Date: Mon Jan 20 2014 - 10:17:39 CST

What i understood is that frames that are similar i.e., within a cutoff of
say some RMSD, should be in the same cluster. The output is number of
clusters specified +1

> 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.
> 

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