I have a question regarding the "critical distance" (epsilon) metrics.
If I correctly understand Shao et al. paper, this metrics can be useful,
among others, to decide the number of clusters. However, when ptraj is
run requiring a certain number of clusters, the critical distance is not
reported (I see the average distance to the centroid within each cluster
but not the distance between the clusters centroids) Or is it?
Now, if we do it the other way round, that is, if we fix epsilon in
ptraj then we end with the same problem we had at the beginning: we need
to choose a certain number of clusters to decide what epsilon to apply,
since there seems not to be a clear-cut criterium for epsilon given a
clustering method. Or I misunderstood something (very possible, even
probable)
I would appreciate insights from more clever and experienced people.
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Le 22/04/13 07:20, Vaibhav Dixit a écrit :
> Hi,
> Did you try other epsilon values like 1.9, 2.0, 2.1, 2.2 or 2.5, 2.6?
>
>
> On Fri, Apr 19, 2013 at 1:44 PM, Amparo Garcia Lopez <
> Amparo.GarciaLopez.unige.ch> wrote:
>
>> Hi Dan,
>>
>> thanks for your reply.
>>
>> So I tried using the sieve option, and I got the same thing: all frames in
>> one cluster. I tried using epsilon (2.3) instead of cluster count and then
>> it created ~200 representative pdb's!
>>
>> Yes, I read the paper you're mentioning back in the day. I'll have to read
>> it again and try some other method, as the average linking isn't making
>> much sense for me. Any suggestions on what to try first?
>>
>> Thanks very much,
>> Amparo
>>
>>
>> Amparo Garcia-Lopez, Ph.D.
>>
>> Pharmaceutical Biochemistry
>> School of Pharmaceutical Sciences
>> University of Geneva
>> Quai Ernest-Ansermet 30
>> 1211 Genève 4 - Switzerland
>>
>> Tel: +41 (0)22 379 3376
>> Fax: +41 (0)22 379 3360
>>
>> e-mail: Amparo.GarciaLopez.unige.ch
>> ________________________________________
>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> Sent: 15 April 2013 16:09
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] clustering places all frames in one cluster
>>
>> Hi,
>>
>> On Mon, Apr 15, 2013 at 2:26 AM, Amparo Garcia Lopez
>> <Amparo.GarciaLopez.unige.ch> wrote:
>>> what I get is 10 clusters in which, 19,991 frames are in the first
>> cluster (c0), and the rest of the clusters have only one point in them.
>>>
>>> This is not possible, I've done clustering of this RNA before using diff
>> settings (e.g., collecting 1 frame every 100 instead of every 20) and I get
>> clusters with nicely distributed occurences.
>>> what do you think I have done wrong? Maybe 10 clusters is too much,
>> maybe collecting 1 every 20 is not a good idea? We are talking about a
>> trajectory of 400 ns here.
>>
>> Clustering is very much an art form; there really is no
>> one-size-fits-all procedure for clustering every trajectory. Settings
>> that work well on one system may give poor results on another (as you
>> have seen). Have you tried varying epsilon instead of cluster count,
>> or trying some of the other clustering algorithms available in ptraj?
>> You can also try the 'sieve' option, which will first cluster on a
>> reduced set (similar to the offset method) then add frames back in
>> based on similarity to cluster centroids. If you haven't yet, I highly
>> recommend you read through the clustering journal article from Shao &
>> Cheatham et al., JCTC (2007) v 3 p 2312-2334.
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 22 2013 - 06:30:03 PDT
