Thanks Dan,
Yeah, if you omit all it just prints everything out at an amber trajectory.
There isn't a way to skip this step (at least in my testing)
What is the best way (how do you) create a 2D rmsd plot? I don't think I
have seen how to do this yet...
Thanks,
Jonathan
On Thu, Jan 8, 2015 at 11:56 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Sorry for the delay in replying - the original ptraj clustering code
> is not mine, so I have far less insight into it's use. I will answer
> your questions as best as I am able.
>
> On Sun, Jan 4, 2015 at 11:05 AM, Jonathan Gough
> <jonathan.d.gough.gmail.com> wrote:
> > Not knowing what the cluster count is, it seems that the best way to
> > proceed is to:
> > 1. run CobWeb (clusters -1) to get an idea of the number (range of
> > numbers) for natural clusters in a given data set (where the atom masks
> are
> > the same)
> > 2. Then run averagelinkage, means, and/or SOM algorithms with cluster
> > values around that implicated by CobWeb and use the pSF and DBI to assess
> > efficacy and choose a specific cluster count. Then proceed with
> analysis...
>
> This may be a good way to go, but my personal feeling is that it is
> overkill. I usually just try to get a good idea for how many clusters
> there are by generating and visualizing a 2d RMS plot.
>
> > I did notice that in the implementation of the agglomerative algorithms
> > the ClusterMerging.txt
> > file gives pSF and DBI values for different numbers of clusters. It was
> > noted that one can set clusters to 1 and then use ReadMerge to generate
> > other numbers of clusters. I'm not sure exactly how to use this type of
> > functionality, but I was wondering, can you just run cluster 1, then use
> > the results generated in ClusterMerging.txt to decide on the number of
> > clusters and critical distance (as per your paper - low DBI and high pSF)
> > for an agglomerative algorithm?
>
> I'm not sure what paper you mean. If you're talking about the Shao
> Cheatham et al. 2007 paper I'm not on that :-). As far as I know the
> 'readmerge' functionality was designed so you could essentially
> "restart" clustering for certain algorithms, e.g. if you stop at 20
> clusters with hierarchical average linkage and want to continue to 10
> you can without having to repeat the previous clustering steps. At any
> rate, the best advice I can give here is to just "try it and see".
>
> > If I am looking to test out and compare different clustering algorithms,
> is
> > there a way to tell ptraj to NOT print out the full clusters? (if all I
> am
> > trying to do is assess the representative structures and the clustering
> > metrics)
>
> I think if you omit the 'all' keyword then ptraj should not print out
> cluster trajectories. Is this not the case?
>
> -Dan
>
> >
> > Any insight would be appreciated.
> >
> > Thanks,
> > Jonathan
> >
> >
> >
> > On Mon, Dec 22, 2014 at 9:59 PM, Jonathan Gough <
> jonathan.d.gough.gmail.com>
> > wrote:
> >
> >> As Always, Very Helpful. Thanks Dan!
> >>
> >> On Mon, Dec 22, 2014 at 9:30 PM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> The ptraj code is still there in Amber 14, it's just not built by
> default.
> >>> You need to go to the AmberTools/src/ptraj subdirectory and type 'make
> >>> install' (after configuring serial of course). Let me know if you hit
> any
> >>> roadblocks.
> >>>
> >>> Hope this helps,
> >>>
> >>> -Dan
> >>>
> >>> On Monday, December 22, 2014, Jonathan Gough <
> jonathan.d.gough.gmail.com>
> >>> wrote:
> >>>
> >>> > That makes sense.
> >>> >
> >>> > Have all the algorithms from your "J. Chem. Theory Comput., Vol. 3,
> No.
> >>> 6,
> >>> > 2007" paper been ported over to cpptraj?
> >>> >
> >>> > I just realized that ptraj is not in Amber14, do you have a
> >>> recommendation
> >>> > on how best to install/compile ptraj (AmberTools13) alongside of a
> >>> > pre-existing Amber14 installation?
> >>> >
> >>> > Thanks,
> >>> > Jonathan
> >>> >
> >>> > On Fri, Dec 19, 2014 at 11:52 AM, Daniel Roe <daniel.r.roe.gmail.com
> >>> > <javascript:;>> wrote:
> >>> >
> >>> > > Hi,
> >>> > >
> >>> > > The pseudo-F calculation is not yet in the released version of
> >>> > > cpptraj, but it has been in the development version for some time.
> It
> >>> > > might possibly be released as part of an update. You could *maybe*
> >>> > > calculate it manually but it would take quite a bit of scripting.
> You
> >>> > > would need to manually calculate the centroid for each cluster and
> a
> >>> > > centroid for all clusters (doing rms-fitting as necessary if that
> is
> >>> > > your distance metric), then calculate the between-group and
> >>> > > within-group sum of squares for each cluster. If for some reason
> you
> >>> > > really need the pseudo-F statistic right away you'll have to use
> >>> > > clustering in ptraj for now.
> >>> > >
> >>> > > -Dan
> >>> > >
> >>> > > On Thu, Dec 18, 2014 at 3:54 PM, Jonathan Gough
> >>> > > <jonathan.d.gough.gmail.com <javascript:;>> wrote:
> >>> > > > Dear All,
> >>> > > >
> >>> > > > Is there a way to compute the pseudo F-statistic
> >>> > > > (pSF), as per J. Chem. Theory Comput., Vol. 3, No. 6, 2007,
> >>> > > > when clustering in cpptraj?
> >>> > > >
> >>> > > > Thanks
> >>> > > > Jonathan
> >>> > > > _______________________________________________
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> >>> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >>> > >
> >>> > >
> >>> > >
> >>> > > --
> >>> > > -------------------------
> >>> > > Daniel R. Roe, PhD
> >>> > > Department of Medicinal Chemistry
> >>> > > University of Utah
> >>> > > 30 South 2000 East, Room 307
> >>> > > Salt Lake City, UT 84112-5820
> >>> > > http://home.chpc.utah.edu/~cheatham/
> >>> > > (801) 587-9652
> >>> > > (801) 585-6208 (Fax)
> >>> > >
> >>> > > _______________________________________________
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> >>> > >
> >>> > _______________________________________________
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> >>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>> >
> >>>
> >>>
> >>> --
> >>> -------------------------
> >>> Daniel R. Roe, PhD
> >>> Department of Medicinal Chemistry
> >>> University of Utah
> >>> 30 South 2000 East, Room 307
> >>> Salt Lake City, UT 84112-5820
> >>> http://home.chpc.utah.edu/~cheatham/
> >>> (801) 587-9652
> >>> (801) 585-6208 (Fax)
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Thu Jan 08 2015 - 09:30:02 PST
