Thanks Ian,
I saw experimental observations and restraints (empirical observations)
as completely different but I now see they are just two different
sources of information that restrain the model parameters. So when you
are counting they can all get "one vote" as long as the observations are
independent. However, from an information content point of view the
weight, or the standard deviation for Fobs, should still matter when
multiple observations/restrains affect a model parameter.
For instance, torsion angle restraints tend to have broad distibutions
leading to low weights and I would expect adding them as observations to
the refinement will not contribute greatly to the "available
information" to define the model, unless there is not much information
from other sources to start with. In the recent posting of using
secondary structure conformational restraints at 3.6A this may start to
make a difference.
Bart
Ian Tickle wrote:
Peter, Bart
Actually the restraint weight doesn't affect the restraint count one
iota and as far as counting is concerned each restraint has exactly one
'vote' in the count. However there is an important proviso: the
restraints must be completely independent to contribute fully to the
count. Suppose you have a torsion restraint say on an methoxyphenyl
group (an example close to my heart since we have endless debates about
it!), and suppose the weight on the restraint is absolutely miniscule,
but still non-zero (we'd better say it's > than the machine precision to
avoid rounding problems). Provided no other restraint or observation
(restraints and observations are of course essentially the same thing)
affects that torsion angle it will have its full effect, in fact the
effect won't depend on the weight. Of course as soon as you have other
restraints which affect that same torsion angle they will compete with
each other depending on their relative weights, and you can't count them
as independent any more.
To answer Peter's original question each *active* restraint is counted.
The question of inactive restraints becomes relevant when considering
e.g. VDW restraints which normally only become active when the distance
becomes less than a threshold.
-- Ian
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bart Hazes
Sent: 14 February 2008 15:53
To: Meyer, Peter
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] counting constraints?
Hi Pete,
In your example it would count as 4 restraints, not constraints, and
certainly not 4 observations or 4 parameters. It is not clear
to me how
to quantify the information content in restraints, it
probably depends
on the type of restraint and surely on the weight. Maybe information
theory has some ideas if you are really interested.
For real constraints, which fix parameters of the model one way or
another, it may be easier. For instance imposing exact NCS 2-fold
symmetry reduces the parameters by a factor of 2.
Bart
Meyer, Peter wrote:
Hi,
The recent discussion on Rwork/Rfree ratio reminded me of
something I was wondering about (*). When counting
constraints as observations for determining the observation
to parameter ratio, is each unique constraint counted, or
each time a given constraint is used. For example, if there
are 4 carbon oxygen bonds (assuming the same parameters,
let's say serine beta-carbon to serine gamma-oxygen), would
this count as 4 constraints as observations, or 1?
Intuitively, it seems to me like it should be counting
unique constraints (although as near as I can tell these
aren't listed in refmac5 logfiles). But I don't have a clear
explanation for why, and of course I could be wrong on this.
Thanks,
Pete
* Rough translation - I'm about to ask another stupid
question. Not like it's the first time.
--
==============================================================
================
Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
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Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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