Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

[Simon Kolstoe]

It can sometimes be struggle to find the boundary between cynicism and  
pragmatism!

I was, however, rather bemused by Dr Joosten's 7 rules of thumb -  
probably all of which I use and have seen used by referees. Of course  
I wouldn't want to blindly advocate any of them, however their use  
does make life somewhat easier for those of us who use crystallography  
to discover things about biology compared with their use by the  
(rather impressive!) members of this community who are involved in  
theoretical/methodological development. A time comes on my projects  
where you have to say two things -  1) "my structure is telling me x  
and although I can spend the next six months performing minor tweaks  
these will not add (or subtract) from the conclusions I am interested  
in" and 2)"when I submit this to referees will they think my structure  
is appropriate to draw these conclusions?". It is whilst asking these  
two questions that rules of thumb become somewhat handy, especially  
when they coincide with the rules of thumb used by the referees.

Simon


On 28 Oct 2010, at 10:28, Eleanor Dodson wrote:

Oh cynic!
Eleanor



On 10/27/2010 09:01 PM, Simon Kolstoe wrote:
Surely the "best" model is the one that the referees for your paper  
are
happy with?

I have found referees to impose seemingly random and arbitrary  
standards
that sometime require a lot of effort to comply with but result in
little to no impact on the biology being described. Mind you  
discussions
on this email list can be a useful resource for telling referee's why
you don't think you should comply with their "rule of thumb".

Simon



On 27 Oct 2010, at 20:11, Bernhard Rupp (Hofkristallrat a.D.) wrote:

Dear Young and Impressionable readers:

I second-guess here that Robbie's intent - after re-refining many  
many
PDB
structures, seeing dreadful things, and becoming a hardened cynic  
- is to
provoke more discussion in order to put in perspective - if not  
debunk-
almost all of these rules.

So it may be better to pretend you have never heard of these  
rules. Your
crystallographic life might be a happier and less biased one.

If you follow this simple procedure (not a rule)

The model that fits the primary evidence (minimally biased electron
density)
best and is at the same time physically meaningful, is the best  
model, i.
e., all plausibly accountable electron density (and not more) is  
modeled.

This process of course does require a little work (like looking
through all
of the model, not just the interesting parts, and thinking what  
makes
sense)
but may lead to additional and unexpected insights. And in almost  
all
cases,
you will get a model with plausible statistics, without any  
reliance on
rules.

For some decisions regarding global parameterizations you have to
apply more
sophisticated test such as Ethan pointed out (HR tests) or Ian uses
(LL-tests). And once you know how to do that, you do not need any
rules of
thumb anyhow.

So I opt for a formal burial of these rules of thumb and a toast to
evidence
and plausibility.

And, as Gerard B said in other words so nicely:

Si tacuisses, philosophus mansisses.

BR

-----Original Message-----
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf  
Of
Robbie
Joosten
Sent: Tuesday, October 26, 2010 10:29 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

Dear Anthony,

That is an excellent question! I believe there are quite a lot of
'rules of
thumb' going around. Some of them seem to lead to very dogmatic
thinking and
have caused (refereeing) trouble for good structures and lack of
trouble for
bad structures. A lot of them were discussed at the CCP4BB so it may
be nice
to try to list them all.


Rule 1: If Rwork < 20%, you are done.
Rule 2: If R-free - Rwork > 5%, your structure is wrong.
Rule 3: At resolution X, the bond length rmsd should be < than Y  
(What is
the rmsd thing people keep talking about?) Rule 4: If your  
resolution is
lower than X, you should not use_anisotropic_Bs/riding_hydrogens
Rule 5: You should not build waters/alternates at resolutions lower
than X
Rule 6: You should do the final refinement with ALL reflections Rule
7: No
one cares about getting the carbohydrates right


Obviously, this list is not complete. I may also have overstated  
some
of the
rules to get the discussion going. Any addidtions are welcome.

Cheers,
Robbie Joosten
Netherlands Cancer Institute

Apologies if I have missed a recent relevant thread, but are  
lists of
rules of thumb for model building and refinement?





Anthony



Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076


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