From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 20 2014 - 10:39:45 CST

On Mon, Jan 20, 2014 at 11:17 AM, <manali_at_bioinfo.net.in> wrote:
>
> 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

that is not correct. your result are 5 clusters and the list of
(remaining) unclustered files. in your case, the 5 clusters are the
first 5 frames, which is the limit for how many clusters measure
cluster will by default be looking for.

you have measured the rmsd to compare the results to, but did you also
align the frames? you should use clustering based on rmsd directly as
clustering criterion to compare to your measurements. or redo the
manual measurements after an alignment.

axel.

>
>
>
>
>> 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
>
>

-- 
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.