AMBER Archive (2008)

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

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Fri May 09 2008 - 15:05:39 CDT

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.
> >
>
> > -----------------------------------------------------------------------
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> >
>
>
> --
> sychen <u8613020_at_mail.ndhu.edu.tw>
>
>

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