AMBER Archive (2008)

Subject: RE: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 13 2008 - 10:08:08 CDT

Hi Dong,

I've not tried clustering analysis with ptraj, however the following
tutorial:

http://ambermd.org/tutorials/basic/tutorial3/index.htm

Section 6, explains how to do clustering of an AMBER trajectory using the
mmtsb toolset.

I hope this helps,
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Dong Xu
> Sent: Monday, May 12, 2008 9:09 PM
> To: amber_at_scripps.edu; Jianyin Shao; sychen
> Subject: Re: AMBER: silhouette width/coefficient after clustering by
> PTRAJ9.9
>
> Hi Jianyin and sychen,
>
> I'm also very interesting in using ptraj to perform clustering
> analysis. However, I wasn't able to locate any documentation on this
> topic, not even on ptraj official web site:
> http://www.chpc.utah.edu/~cheatham/ptraj.html
>
> Maybe I have missed something here, would you please email some
> instructions as well as the scripts that calculate the silhouette
> width?
>
> Many thanks!
>
> Dong Xu
>
> On Fri, May 9, 2008 at 1:05 PM, Jianyin Shao <jyshao2004_at_gmail.com> wrote:
> > Hi, sychen,
> >
> > I think we did replace the mask parser with a new one. I didn't realize
> this
> > discrepancy.
> > I would suggest you to use "@461-474,494-507" under the new version. If
> you
> > insist using the old parser, you can replace the call of function
> > processAtomMaskDetailedVH() back to processAtomMaskDetailed() in lines
> 1352
> > and 1359 in ptraj.c file.
> >
> > Please send me a copy of your failed SOM clustering script.
> >
> > Best,
> >
> > Jianyin
> >
> >
> > On 5/8/08, sychen <u8613020_at_msg.ndhu.edu.tw> wrote:
> > > Hi, Jianyin Shao,
> > > Thank you for your kind help. It works fine.
> > > However I got 2 problems in PTRAJ,
> > > 1. Does atom selection differ in the latest version?
> > > \-/ Version: "AMBER 9.0 integrated" (April 2006)
> > > -/- Executable is: "ptraj"
> > > /-\
> > > \-/ Residue labels:
> > >
> > > (omit)
> > >
> > > PTRAJ: matrix mwcovar name a16a17.covar @461-_at_474,@494-_at_507 mass
> > > Mask [@461-_at_474,@494-_at_507] represents 28 atoms
> > >
> > >
> > > \-/
> > > -/- PTRAJ: a utility for processing trajectory files
> > > /-\
> > > \-/ Version: "Cheatham lab development full version 9.9g" (1 April
> > 2008)
> > > -/- Executable is: "ptraj"
> > > /-\
> > > \-/ Residue labels:
> > >
> > > (omit)
> > >
> > > PTRAJ: matrix mwcovar name a16a17.covar @461-_at_474,@494-_at_507 mass
> > > Mask [@461-_at_474,@494-_at_507] represents 4 atoms
> > >
> > > I also trid the latest version 9.9h, and the result was as same as
> 9.9g
> > gave.
> > >
> > > 2. Does there any paticular environment to be modify before compiling
> > PTRAJ 9.9g(h)?
> > > The clustering always fail as SOM algorithm was used and the error
> > message was as follows,
> > >
> > > The first pass through the trajectory is complete.
> > > Clustering using the SOM algorithm.
> > > --------------------------------------------------------------------
> > > Error in file cluster.c line 6520 when calling SafeMalloc() to alloc
> of
> > -547749984 bytes.
> > >
> > >
> > >
> > > Sincerely,
> > > sychen
> > >
> > >
> > > On Fri, 2 May 2008 17:27:44 -0600
> > > "Jianyin Shao" <jyshao2004_at_gmail.com> wrote:
> > >
> > > > Hi, sychen,
> > > >
> > > > Attached is a perl script to calculate the silhouette width for the
> > ptraj clustering output.
> > > > Please run "silhouette.pl -h" to see the usage. If you have any
> > questions or suggestions, please let me know. If I incorporate the code
> into
> > the ptraj, I will let you know.
> > > >
> > > > Thanks,
> > > >
> > > > JS
> > > >
> > > > On 5/2/08, sychen <u8613020_at_msg.ndhu.edu.tw> wrote: Dear all,
> > >
> > >
> > >
> > > > I need a program or script to calculate silhouette
> > width/coefficient
> > > > after clustering by PTRAJ9.9, because I'd like to make for
> sure
> > of the
> > > > quality of clustering numbers/algorithms and I could not find
> > such
> > > > function included in PTRAJ so far.
> > > > Thank you very much!
> > > >
> > > >
> > > >
> > > > Best regards,
> > > > sychen.
> > > >
> > > >
> > -----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber_at_scripps.edu
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> > > >
> > > >
> > >
> > >
> > > --
> > > sychen <u8613020_at_mail.ndhu.edu.tw>
> > >
> > >
> >
> >
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