[prev in list] [next in list] [prev in thread] [next in thread] 

List:       relax-devel
Subject:    Re: [sr #2402] high SSE values with Model Free runs
From:       "Edward d'Auvergne" <edward () domain ! hid>
Date:       2009-08-06 16:13:47
Message-ID: 7f080ed10908060913m609b4da8u58c1a13bf189480f () domain ! hid
[Download RAW message or body]

Hi,

A simple test for this would be to use the relax optimisation (minfx,
https://gna.org/projects/minfx/) rather than Art Palmer's Modelfree4
as an optimisation engine, and then see if you get the same result.
Note that the SSE values are dependent on two things - the more data
the higher the value; and the smaller the relaxation data errors, the
larger the SSE.  The high SSE values would only be a relax bug if
relax is feeding the wrong data and errors to Modelfree4, otherwise
the bug will be in Modelfree4 itself.  The absolute value of the
number doesn't really say much, but I would recommend using the Newton
optimisation algorithm in relax through the 'full_analysis.py' script
and then you can compare the result (to understand my bias, please see
my papers or my PhD thesis at http://www.nmr-relax.com/refs.html ;).
I hope this helps.

Regards,

Edward


On Tue, Aug 4, 2009 at 4:47 PM,
anonymous<NO-REPLY.INVALID-ADDRESS@gna.org> wrote:
>
> URL:
> =A0<http://gna.org/support/?2402>
>
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Summary: high SSE values with Model Free =
runs
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Project: relax
> =A0 =A0 =A0 =A0 =A0 =A0Submitted by: None
> =A0 =A0 =A0 =A0 =A0 =A0Submitted on: Tuesday 08/04/2009 at 16:47 CEST
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Category: None
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Priority: 5 - Normal
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Severity: 3 - Normal
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Status: None
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Privacy: Public
> =A0 =A0 =A0 =A0 =A0 =A0 Assigned to: None
> =A0 =A0 =A0 =A0Originator Email: mikaela.stewart@domain.hid
> =A0 =A0 =A0 =A0 =A0 =A0 Open/Closed: Open
> =A0 =A0 =A0 =A0 Discussion Lock: Any
> =A0 =A0 =A0 =A0Operating System: GNU/Linux
>
> =A0 =A0_______________________________________________________
>
> Details:
>
> I am using relax to run Palmer's model free. =A0The program converges aft=
er a
> normal number of rounds (9-15) and gives me S2, te, Rex etc that agree wi=
th
> the literature for the proteins I'm working with. =A0However, the SSE val=
ues
> seem abnormally high. =A0There are a few low values (<2) but a majority a=
re
> greater than 20 with some as high as 300. =A0Have I made a mistake in run=
ning
> the program or am I misinterpreting the values? =A0I've tried using repor=
ted
> data from the literature and I have the same problem that I get when runn=
ing
> my data for my protein of interest. =A0Thank you for your help.
>
>
>
>
> =A0 =A0_______________________________________________________
>
> Reply to this item at:
>
> =A0<http://gna.org/support/?2402>
>
> _______________________________________________
> =A0Message sent via/by Gna!
> =A0http://gna.org/
>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
> This is the relax-devel mailing list
> relax-devel@domain.hid
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-devel
>


[prev in list] [next in list] [prev in thread] [next in thread]