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 per
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
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:
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
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 wea
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 than the other se
[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
> "t
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 cal
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 inva
I've looked at about 10 cases where structures have been refined in lower
symmetry space groups. When you make the NCS operators into crystallographic
operators, you don't change the refinement much, at least in terms of
structural changes. That's the case whether NCS restraints have been appl
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 an
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 interesting for begin
s), and thus miss potentially valuable information.
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Dirk Kostrewa
> Sent: 08 February 2008 10:10
> To: CCP4BB
> Subject: Re: [ccp4bb] an over refined structure
>
> Dear Da
ECTED] 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
andom selection or Rfree + NCS
(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 <mailto:CCP4BB@JISCMAIL.AC.
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 <mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference
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
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 righ
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 genera
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 inab
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 s
al 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 <mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree
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%. Th
mix Rwork and Rfree sets. Normal random selection or Rfree + NCS
(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: CCP4B
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 th
sage-
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 ac
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
---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 <mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rf
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 she
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 as a criteria for
structure correctn
m selection or Rfree + NCS
(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 ov
-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 agree that the difference in Rwork to Rfree is quite acceptable at
your resolution
have opinions on how many
waters you expect 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 s
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 refl
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
porting I think the latter is
very unlikely, possibly you just need to tweak 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 Shaana
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
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 reso
you are reporting I think the latter is
very unlikely, possibly you just need to tweak 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
What is the resolution? Are you using ncs restraints (you probably
should, on the coordinates but not on the Bs)? How does your
Ramachandran plot look?
You might tighten the geometry even more. Aside from all theoretical
arguments about how big the rmsd's should be, if they're rather
loose, t
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 ?
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 P
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 jus
amachandran outliers, etc., map) are OK you should
just be happy with your structure.
Cheers,
Boaz
- Original Message -
From: Sun Tang <[EMAIL PROTECTED]>
Date: Monday, February 4, 2008 18:41
Subject: [ccp4bb] an over refined structure
To: CCP4BB@JISCMAIL.A
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.
What
45 matches
Mail list logo
