Dale Tronrud wrote:
In summary, this argument depends on two assertions that you can
argue with me about:
1) When a parameter is being used to fit the signal it was designed
for, the resulting model develops predictive power and can lower
both the working and free R. When a signal is
Edward Berry wrote:
Dirk Kostrewa wrote:
Dear Dean and others,
Peter Zwart gave me a similar reply. This is very interesting
discussion, and I would like to have a somewhat closer look to this to
maybe make things a little bit clearer (please, excuse the general
explanations - this might be
Dale Tronrud wrote:
In summary, this argument depends on two assertions that you can
argue with me about:
1) When a parameter is being used to fit the signal it was designed
for, the resulting model develops predictive power and can lower
both the working and free R. When a
PROTECTED] On
Behalf Of
Eleanor Dodson
Sent: Tuesday, February 05, 2008 3:38 AM
To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree is quite acceptable
at your resolution. You cannot/ should
-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Eleanor Dodson
Sent: Tuesday, February 05, 2008 3:38 AM
To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree is quite acceptable
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree is quite
acceptable at your resolution. You cannot/ should not use
Rfactors as a criteria for structure correctness.
As Ian points out - choosing a different Rfree set of
reflections
Back in the old days, when I worked on crystal structures with 15 or
20 atoms or so, the symptoms of missed crystallographic symmetry
included instability of the refinement, high correlations between
parameters, and (relatively) large deviations between equivalent bond
distances and bond
Rotational near-crystallographic ncs is easy to handle this way, but
what about translational pseudo-symmetry (or should that be
pseudo-translational symmetry)? In such cases one whole set of spots
is systematically weaker than the other set. Then what is the
theoretically correct way to
[EMAIL PROTECTED] wrote:
Rotational near-crystallographic ncs is easy to handle this way, but
what about translational pseudo-symmetry (or should that be
pseudo-translational symmetry)? In such cases one whole set of spots is
systematically weaker than the other set. Then what is the
In such cases, we always define the test set first in the high-symmetry
space group choice. Then, if it is warranted to lower the
crystallographic
symmetry and replace with NCS symmetry, we expand the test set
to the lower symmetry space group. In other words, the test set itself
will be
Bart Hazes wrote:
Dale Tronrud wrote:
[EMAIL PROTECTED] wrote:
Rotational near-crystallographic ncs is easy to handle this way, but
what about translational pseudo-symmetry (or should that be
pseudo-translational symmetry)? In such cases one whole set of
spots is
systematically weaker
Bottom line: thin shells are not a perfect solution, but if NCS is
present, choosing the free set randomly is *never* a better choice,
and almost always significantly worse.
hmmm ... I wonder if that is true. For low order NCS (two- three-
fold, even five-fold) I don't believe that thin
@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree is quite acceptable at
your resolution. You cannot/ should not use Rfactors as a criteria for
structure correctness.
As Ian points out - choosing a different Rfree set
Actually the bottom lines below were my argument in the case
that you DO apply strict NCS (although the argument runs into
some questionable points if you follow it out).
In the case that you DO NOT apply NCS, there is a second
decoupling mechanism:
Not only the error in Fo may be opposite for
To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree is quite acceptable
at your resolution. You cannot/ should not use Rfactors as a
criteria for structure correctness.
As Ian points out - choosing
PROTECTED] On Behalf Of
Eleanor Dodson
Sent: Tuesday, February 05, 2008 3:38 AM
To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree is quite acceptable at
your resolution. You cannot/ should not use Rfactors
Hi Ed,
This is an intriguing argument, but I know (having caught such a case as
a reviewer) that even in cases of low NCS symmetry, Rfree can be
significantly biased. I think the reason is that the discrepancy between
pairs of NCS-related reflections (i.e. Fo-Fo') is generally
significantly
Dear Ed,
I don't see how you decouple symmetry mates in the case of a wrong
space group. Symmetry mates should agree with each other typically
within R_sym or R_merge percent, eg; about 2-5% . Observed and
calculated reflections agree within R_Factor of each other, so about
20-30%. The
Dean Madden wrote:
Hi Dirk,
I disagree with your final sentence. Even if you don't apply NCS
restraints/constraints during refinement, there is a serious risk of NCS
contaminating your Rfree. Consider the limiting case in which the
NCS is produced simply by working in an artificially low
Agreed, and this is even more true if you consider R-merge is calculated
on I's and Rfree on F's, Rmerge of 5% should contribute 2.5% to Rfree;
and furthermore errors add vectorially so it would be
more like ,025/sqrt(2).
I guess I have to take all those other errors that have to do with
the
If you think about it, there is an analogy to relaxing geometrical
constraints, which also allows the refinement to put atoms into
density. The reason it usually doesn't help Rfree is that the density
is spurious. At least some of the incorrect structure determinations of
the early 90's (that
(especially 4x or higher) will drive Rfree down unfairly.
Doug Ohlendorf
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Eleanor Dodson
Sent: Tuesday, February 05, 2008 3:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I
Hi Phil,
Here I will disagree. R-free rewards you for putting in atom in density
which an atom belongs in. It doesn't necessarily reward you for putting
the *right* atom in that density, but it does become difficult to do
that under normal circumstances unless you have approximately the
Dean Madden wrote:
Hi Ed,
This is an intriguing argument, but I know (having caught such a case as
a reviewer) that even in cases of low NCS symmetry, Rfree can be
significantly biased. I think the reason is that the discrepancy between
pairs of NCS-related reflections (i.e. Fo-Fo') is
:[EMAIL PROTECTED] On Behalf
Of
Eleanor Dodson
Sent: Tuesday, February 05, 2008 3:38 AM
To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree is quite acceptable
at your resolution. You cannot/ should
Hi Sun,
On Mon, Feb 04, 2008 at 02:15:05PM -0800, Sun Tang wrote:
I used NCS before rigid body refinement. After that I did not put
NCS restraints in the restrained refinement and TLS+restrained
refinement because it raised the R/Rfree quite a lot.
Use NCS. Really!
There is never a reason
I agree that the difference in Rwork to Rfree is quite acceptable at
your resolution. You cannot/ should not use Rfactors as a criteria for
structure correctness.
As Ian points out - choosing a different Rfree set of reflections can
change Rfree a good deal.
certain NCS operators can relate
to find at various resolutions.
HTH
-- Ian
-Original Message-
From: Sun Tang [mailto:[EMAIL PROTECTED]
Sent: 04 February 2008 22:32
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] an over refined structure
Hi Ian,
Thank you very much for your detailed
Hi -
I don't think there is something necessarily wrong with the values
you report.
A few questions to see *if* something is wrong are:
- as you wrote to Tim you have NCS: do you use NCS restraints ?
- what is the resolution / B factor of the data ?
- have the data been checked for twining
I would agree that the difference is suspiciously high. I. Tickle and
others have published analytical expressions for how to estimate the ratio
between R and Rfree, just google for tickle rfree to find the
references.
You easily achieve a large difference by adding too many waters which just
the X-ray and/or restraint
weights.
HTH
Cheers
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sun Tang
Sent: 04 February 2008 16:56
To: Boaz Shaanan
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
Hi Boaz
Hi Tim,
Thank you for your and information and suggestions. There are two indepdent
molecules in the asymmetric unit and one molecule does not have very good
density, especially in the N-terminus.
Do you think that I should remove the region in the refinement?
Best,
Sun
Tim Gruene [EMAIL
Hello All,
I refined a structure with Refmac in CCP4i and the R/Rfree is 0.215/0.277. The
difference between R and Rfree is too much even though I used 0.01 for
weighting term in the refinement (the default value is 0.3). The RMSD for bond
length and bond angle is 0.016 A and 1.7 degree.
Dear Sun,
If we take Ian's formula for the ratio of R(free) to R(work) from his
paper Acta D56 (2000) 442-450 and make some reasonable approximations,
we can reformulate it as:
R(free)/R(work) = sqrt[(1+Q)/(1-Q)] with Q = 0.025pd^3(1-s)
where s is the fractional solvent content, d is the
weights.
HTH
Cheers
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sun Tang
Sent: 04 February 2008 16:56
To: Boaz Shaanan
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
Hi Boaz,
Thank you for your
Hi Anastassis,
Thank you very much for your suggestions. I answered the questions as follows.
I used NCS before rigid body refinement. After that I did not put NCS
restraints in the restrained refinement and TLS+restrained refinement because
it raised the R/Rfree quite a lot.
The resolution is
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