Hi,
I see what you mean now. So without seeing your cluster data myself
(something like your cluster population vs time data) I can't be
certain, but I suspect you may be encountering "noise" frames, i.e.
frames that do not belong to any specific cluster. Could that be the
case?
-Dan
On Thu, Jun 13, 2019 at 6:01 PM Daniel Fernández Remacha
<dnlfr1994.gmail.com> wrote:
>
> Thank you very much for your answers. However I think I did not express
> correctly. My question goes in another sense.
>
> For what I know, cluster plots usually start at the maximum of the y axis
> (1), meaning all conformations belong to the same cluster until the moment
> where another cluster is found; where the first starts to decrease as the
> second increases, and so on.
>
> In my case, pop1 starts at the bottom of the y axis and rapidly increases,
> without reaching the unit. Then everything is as expected. But what I don't
> understand is why dbscan does not assume the 100% of the data as part of
> the first cluster. Where does that difference come from?
> Is this behaviour normal?
>
> Hope I explained better this time.
>
> Thank you again,
>
> El jue., 13 jun. 2019 21:50, Daniel Roe <daniel.r.roe.gmail.com> escribió:
>
> > On Thu, Jun 13, 2019 at 3:45 PM Thomas Cheatham <tec3.utah.edu> wrote:
> > >
> > > Perhaps my fault, C programmer... Easy fix +1 or convert to FORTRAN
> >
> > Ha, never! I wish everything started from 0...
> >
> > >
> > > > On Jun 13, 2019, at 9:12 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > > >
> > > > Hi,
> > > >
> > > > Historically, PTRAJ always numbered clusters starting from 0 and
> > > > sorted by population (cluster 0 = most populated). CPPTRAJ has
> > > > continued this convention. All cluster output should have a cluster 0.
> > > >
> > > > -Dan
> > > >
> > > >> On Thu, Jun 13, 2019 at 1:04 PM <dnlfr1994.gmail.com> wrote:
> > > >>
> > > >> Dear users,
> > > >>
> > > >>
> > > >>
> > > >> I am currently working on clustering analysis of several MD with a
> > system
> > > >> with 600 aminoacids for 200 ns simulations.
> > > >>
> > > >> I have plotted the kdist plots for kdist 1 to 10 and from this results
> > > >> obtained I use the following input:
> > > >>
> > > >>
> > > >>
> > > >> cluster C0 dbscan minpoints 4 epsilon 1 sievetoframe rms :1-279 sieve
> > 10 \
> > > >>
> > > >> out dbscan_clust/cnumvtime.dat sil Sil \
> > > >>
> > > >> summary dbscan_clust/summary.dat info dbscan_clust/info.dat \
> > > >>
> > > >> cpopvtime dbscan_clust/cpopvtime.agr normframe repout
> > > >> dbscan_clust/rep repfmt pdb \
> > > >>
> > > >> singlerepout dbscan_clust/singlerep.nc singlerepfmt netcdf
> > avgout
> > > >> Avg avgfmt restart
> > > >>
> > > >> run
> > > >>
> > > >> clear all
> > > >>
> > > >>
> > > >>
> > > >> The clustering runs OK with no noticeable problems. However, it has me
> > > >> intrigued to see that unlike all other clustering plots I have seen
> > > >> (clusters starting at 1), the clusters on this one start from cero. I
> > fail
> > > >> to find a reason for this behaviour. Find a picture of the pop vs
> > frame I
> > > >> get at the bottom of this message.
> > > >>
> > > >>
> > > >>
> > > >> I would really appreciate it if anyone could help me solve this
> > problem
> > > >>
> > > >>
> > > >>
> > > >> Thank you in advance,
> > > >>
> > > >>
> > > >>
> > > >> Daniel Fernández
> > > >>
> > > >>
> > > >>
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Received on Fri Jun 14 2019 - 07:00:04 PDT
