Hi Jonathan,
and thank you so much for taking the time to explain. This is as I suspected,
now I would like to find out more on how it is computed: Do restraint
violations enter this figure? Which "information" is there to support a piece
of alignment in a remote homologue, do alignment scores enter, how is it
computed for insertions, etc? Is there any place where I can read up on how
this figure is computed in Modeller?
Unlike in crystallography, there is no "experimental" evidence for any of my
modeled atomic positions, which is why the analogy makes sense but leaves me
clueless on which information enters the "modeling confidence factor".
If there is any way for me to do the homework myself by reading up I would
happily pick up anything that is suggested.
margot
On Wednesday 09 July 2003 18:42, you wrote:
> Hi,
>
> The B-factor also known as the confidence factor in
> homology modeling, is practically based on the amount
> of information that supports each region of the model.
>
> It is a measure of uncertainty so, high value implies
> low confidence about a specific part of the model. (In
> crystallography, high B-factor imply uncertainty in
> assignment of atom positions).
>
> Note that large B factors are assigned to atoms or
> residues built without a template, including loops,
> reflecting the lack of template support for those
> parts of the model.
>
> cheers,
> ./jonathan
>
>
>
> --- Margot Ernst <> skrev: >
> Hi Modeller community,
>
> > unfortunately I have not received any answer, so I
> > will repeat my question as
> > I REALLY would like to know: What is the value in
> > the B-factur column of the
> > structure files Modeller generates?
> > Thanks for your help,
> > margot
> > --
>
> -----------------------------------------------------------------
>
> > | Dr. Margot Ernst
> > |
> > | Abteilung Prof. Sieghart
> > |
> > | Institut f. Hirnforschung/brainresearch institute
> > |
> > | Spitalgasse 4
> > |
> > | A-1090 WIEN VIENNA, Austria
> > |
> > |
> > |
> > | visit http://www.univie.ac.at/brainresearch
>
> -----------------------------------------------------------------
>
> > the bottom line to brainresearch:
> > If the brain was so simple that you could understand
> > it,
> > you would be so simple that you couldn't. (unknown)
>
> ---------------------------------------------------------
>
> > "Research: If it worked the first time,
> > they would just call it 'search'." -Roy Garcia
>
> --------------------------------------------------------
>
> -----------------------------------------------------------------
>
>
>
> _____________________________________________________
> Gå före i kön och få din sajt värderad på nolltid med Yahoo! Express
> Se mer på: http://se.docs.yahoo.com/info/express/help/index.html
--
-----------------------------------------------------------------
| Dr. Margot Ernst
| Abteilung Prof. Sieghart
| Institut f. Hirnforschung/brainresearch institute
| Spitalgasse 4
| A-1090 WIEN VIENNA, Austria
|
| visit http://www.univie.ac.at/brainresearch
-----------------------------------------------------------------
the bottom line to brainresearch:
If the brain was so simple that you could understand it,
you would be so simple that you couldn't. (unknown)
---------------------------------------------------------
"Research: If it worked the first time,
they would just call it 'search'." -Roy Garcia
--------------------------------------------------------
-----------------------------------------------------------------