funny how always the same questions re-occur ...
anyways, in theory i guess we all agreed long time ago that isd
(inferential structure determination) is the way to go. in practice,
not much has happened in that direction other than mike drawing
spheres.
in my eyes, a theoretically sound scale roughly by the number of
voxels, which is the amount of information. a fudge solution would
probably be a scale ~N, which i also did for the saxs restraint.
however, as the solution of scaling different kinds of restraints is
not really solved anyways, i do not quite see the point of putting a
pre-fixed solution, as it pretends to have found a solution for
something where it has actually not been found.
cheers
frido
On Mon, Jun 8, 2009 at 8:59 PM, Daniel Russel <> wrote:
>
>> This is just basic physics - most restraints are extensive, in that they
>> scale with the system size (e.g. excluded volume, stereochemistry). Any
>> CC-like restraint is intensive, and doesn't scale with system size.
>
> I wouldn't say it has anything to do with physics, but yes, it is obvious
> once you look at it :-)
>
>> Obviously that doesn't work when you combine the two.
>
> The challenge is either making sure people pay attention to to the issue
> early on or making it go away as a problem so IMP developers don't have to
> help them individually :-)
>
>
>> For EM we solved this years ago with a scaling factor. Ideally the scale
>> would simply be N^2 where N is the number of particles in the system.
>
> Why quadratic rather than linear?
>
>> I don't much like the idea of scaling "regular" restraints by the number
>> of atoms or similar, since that would break pretty much everything else
>> where the assumption is made that the sum of the restraints is a score
>> that can be safely minimized
>
> I don't see that being able to minimize the score cares about whether it
> increases as you add atoms
> - for most cases the number number of atoms is constant or otherwise not
> interesting (ie if you are docking proteins you don't want a larger protein
> to automatically score worse)
> - and if you care about minimizing the number of atoms, you can always add
> that as a term in your scoring function
>
>> (this assumes that the score does increase
>> as you add atoms, and restraints on multiple atoms should have more
>> weight than those on just pairs).
>
> Currently the weight scales with the number of particles rather than the
> number of atoms. The convention I proposed would make it scale with the
> number of atoms.
>
> A key invariant is that changing the resolution of the representation should
> not change things too much.
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>
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>
>
--
--
Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried
Tel: +49 89 8578 2651
Fax: +49 89 8578 2641
www.tomotronic.org