Dear Robbie,
Rules 3-5 I found could be approached using my previous rule of thumb. If
anisotropy reduced Rfree by more than half the reduction in R, then I liked it.
It helped me decide to introduce anisotropy for xenon, iodine and chlorine
atoms (supported by non-spherical omit electron de
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
Hi Ed,
I have four of those
http://www.newegg.com/Product/Product.aspx?Item=N82E16822136514
and would now buy these
http://www.newegg.com/Product/Product.aspx?Item=N82E16822136764
DELLete it, I mean the quote you have and shop somewhere else.
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School
On Tue, Oct 26, 2010 at 09:52:51PM -0400, Edward A. Berry wrote:
> Another question about computer hardware- If I configure a computer at
> the Dell site, it costs about $700 to add a 2TB SATA drive. On
> amazon.com or Staples or such, a 2TB drive costs ~$110. to $200 depending
> on brand.
>
> Ar
Don't get ripped off by Dell! Their drives aren't any faster or better
quality than the competition (IMHO they're probably slower and/or lower
quality). If you're looking for a 2 terabyte drive, I have seven Hitachi
7K2000 2 TB (http://www.newegg.com/Product/Product.aspx?Item=N82E16822145298)
dri
Another question about computer hardware- If I configure a computer at the
Dell site, it costs about $700 to add a 2TB SATA drive.
On amazon.com or Staples or such, a 2TB drive costs ~$110. to $200
depending on brand.
Are the Dell-installed drives much faster, or more reliable, or have
a better w
Hi Ian,
Yes, I guess my rule does work as you say.
If, starting the day from (Rwork = 20, Rfree = 30) abbreviate (20,30),
you do something to get (18,29), yes this means that that something was
a bare minimum acceptable thing to do.
If you do something to get (16,29) (decreased R by 4,
Hello All,
Not long ago I posted for some help with my twinned dataset at 1.95 A, and have
confirmed the twinning of P6(5) into P6(5)22. Molecular replacement was
successful and the twin refinement in Refmac yieled R/Rfree of 21%/26%, with a
twin fraction of 0.46.
Although the electron densit
Some time ago, I computed the mean value of Rcryst(F) / Rmerge(F) across the
whole PDB. This average was 4.5, and I take this as a rough estimate of
|Fcalc - Fobs| / sigma(Fobs). More recently, I have been looking in more
detail at deposited data, but so far the few cases where this ratio is clos
On Tuesday, October 26, 2010 04:31:24 pm James Holton wrote:
> Yes, but what I think Frank is trying to point out is that the difference
> between Fobs and Fcalc in any given PDB entry is generally about 4-5 times
> larger than sigma(Fobs). In such situations, pretty much any standard
> statistica
Janet Newman wrote a review on improving diffraction a few years back:
http://dx.doi.org/10.1107/S0907444905032130
it is open access.
Probably the most underappreciated aspect of diffraction is the purity of
the protien. This is because "impurities" like slightly misfolded versions
of your "nativ
- Original Message -
From: James Holton
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, October 26, 2010 6:31 PM
Subject: Re: [ccp4bb] Against Method (R)
Yes, but what I think Frank is trying to point out is that the difference
between Fobs and Fcalc in any given PDB entry is gen
Yes, but what I think Frank is trying to point out is that the difference
between Fobs and Fcalc in any given PDB entry is generally about 4-5 times
larger than sigma(Fobs). In such situations, pretty much any standard
statistical test will tell you that the model is "highly unlikely to be
correct
I found a practical solution to a similar problem. When I get large
gap between Rf/R in refmac I repeat the refinement in PHENIX using the
same model and the same mtz file, It has always worked for me. And I
have no theory for that observation, but the tables in publications
looked better.
>
> Hi.
>
> Here is some additional information.
>
> 1. The purification method that I used included Ni, tag cleavage, and SEC as
> a final step. I have tried samples from three different purification batches
> that range in purity, and even the batch with the worst purity seems to
> produ
Hi.
Here is some additional information.
1. The purification method that I used included Ni, tag cleavage, and SEC
as a final step. I have tried samples from three different purification
batches that range in purity, and even the batch with the worst purity seems
to produce crystals.
2. The pr
On Tuesday, October 26, 2010 01:16:58 pm Frank von Delft wrote:
>Um...
>
> * Given that the weighted Rfactor is weighted by the measurement errors
> (1/sig^2)
>
> * and given that the errors in our measurements apparently have no
> bearing whatsoever on the errors in our models (for macromo
Seeding! Make seeds, rescreen with seeds. Look in many former ccp4bb posts for
references about this.
Jacob
- Original Message -
From: Jürgen Bosch
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, October 26, 2010 3:47 PM
Subject: Re: [ccp4bb] Help with Optimizing Crystals
You d
You did check on a gel that they are indeed your protein ?
If you have sufficient amounts available try digesting it with various
proteases and see if you can identify a stable fragment.
A less radical approach, which might not be accessible to you, you could screen
your protein for alternative
First piece of advice I have is to shove them in the beam and see what
happens. A few days ago we got high-resolution data from crystals that are
shaped like eggs. No edges on them whatsoever. In the past, saucer-shaped
crystals diffracted to 2A whereas their hexagonal 'perfect' cousins (grown
from
Hi Matt,
You'll probably get many different answers to a question like this, but what I
would do is go back to your protein and make different constructs; chop off
termini, surface mutations etc, maybe cleave off the tag. Of course more
screening and optimization might work, but my sense is tha
Hello.
I have obtained disk shaped crystals of a protein that I am working on. I
got hits in about 10 different conditions, with a few common precipitants
and pHs, and I have optimized two conditions so far. In the optimized
conditions, the crystals appear overnight, usually surrounded by or hid
Um...
* Given that the weighted Rfactor is weighted by the measurement errors
(1/sig^2)
* and given that the errors in our measurements apparently have no
bearing whatsoever on the errors in our models (for macromolecular
crystals, certainly - the "R-vfactor gap")
is the weighted Rfactor
Indeed, see: http://scripts.iucr.org/cgi-bin/paper?a07175 .
The Rfree/Rwork ratio that I referred to does strictly use the
weighted ('Hamilton') R-factors, but because only the unweighted
values are given in the PDB we were forced to approximate (against our
better judgment!).
The problem of cour
W C Hamilton "Significance tests on the crystallographic R factor"
Acta Cryst. (1965). 18, 502-510
Interestingly enough, I have used the Hamilton tests in Rietveld powder
refinements of small molecules/intermetallics before before. One problem
were partial occupancies vs split conformations in HT
Dear all,
Augustine, "Confessions", Book 11 Chap. XIV, has it:
"If no one ask of me, I know; if I wish to explain to him who asks, I
know not."
With best wishes,
Gerard.
--
On Tue, Oct 26, 2010 at 01:30:11PM -0500, Phoebe Rice wrote:
> Another issue with the
On Tuesday, October 26, 2010 09:46:46 am Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> Hi Folks,
>
> Please allow me a few biased reflections/opinions on the numeRology of the
> R-value (not R-factor, because it is neither a factor itself nor does it
> factor in anything but ill-posed reviewer's c
Another issue with these statistics is that the PDB insists on a single value
of "resolution" no matter how anisotropic the data. Especially in the
outermost bins, Rmerge could be ridiculously high simply because the data only
exist in one out of 3 directions.
Phoebe
===
Hi Folks,
Please allow me a few biased reflections/opinions on the numeRology of the
R-value (not R-factor, because it is neither a factor itself nor does it
factor in anything but ill-posed reviewer's critique. Historically the term
originated from small molecule crystallography, but it is only a
Yes! - the critical piece of information that we're missing is the
proportion of *all* structures that come from SG centres. Only
knowing that can we do any serious statistics ...
-- Ian
On Tue, Oct 26, 2010 at 5:07 PM, Frank von Delft
wrote:
>> b) very large Rmerge values:
>>
>> Rmerge
b) very large Rmerge values:
Rmerge Rwork Rfree Rfree-Rwork Resolution
-
0.9990 0.1815 0.20860.0271 1.80<<< SG center, unpublished
0.8700 0.1708 0.22700.0562 1.96<<< unpublished
0.7700 0.1870 0.2297
Apologies for not seen the original post, but
$warpbin/arp_warp <
Hi Dirk,
may be too late... but (may be) better later than never -:)
Here is the working example of how you can do it. Note, the
procedure just builds the dummy atoms in spheres with user-defined
centers and radia. You can s
Jackie
I agree completely with Ed (for once!), not only for the reasons he
gave, but also that it's valid to compare statistics such as
likelihood and R factors ONLY if only the model is varied. Such a
comparison is not valid if the data used are varied (in this case you
are changing the data by
Anthony,
Your rule actually works on the difference (Rfree - Rwork/2), not
(Rfree - Rwork) as you said, so is rather different from what most
people seem to be using.
For example let's say the current values are Rwork = 20, Rfree = 30,
so your current test value is (30 - 20/2) = 20. Then accord
Jackie,
please note that (at least imho) the desire to obtain "better" R-factors
does not justify excluding data from analysis. Weak reflections that
you suggest should be rejected contain information, and excluding them
will indeed artificially lower the R-factors while reducing the accuracy
of
On 08/20/2010 05:50 PM, Charles W. Carter, Jr wrote:
Is there a program that will read in a pdb coordinate file and re-order the
side chain atoms in each residue according to a standard order?
I've a program that compares two files for the same structure, but requires
that the order of the ato
I would expect such a difference with lowish resolution data.
Your model will be biased towards the restraints - ie the geometry
willbe good, but there is bearly enough observations to fit the
actualmodel properly. eg - it will be hard to position solvent, and to
recognise any deviaions from N
I'm not sure that "a lttle worse" is the appropriate description - I
think all you can say is that it deviates from the average when only
resolution is used to define what is "average". My point is that a
number of other factors are known to be involved and so you can't say
that this deviation is
Rakesh
Looking at the
http://www.pdbe.org/statistics
Structure Statistics
Then for all structures a we see that Rdiff of > 0.7 is not that uncommon
with this about 1 sigma away from the mean value of 0.4 for all structutures
and 0.45 for your resolution range
For structures with Rdiff ra
Dear all,
Sorry to come back late, when the discussion is over, with one more remark
relevant to the bulk solvent modeling.
I've just got a comment by a colleague of mine, Adam Ben-Shem, who kindly
agreed that I post his message (below) to CCP4bb.
I think he is completely right saying that the
Dear Rakesh, dear Artem,
Since the initial question is not precise (which kind of comments are
expected?) I may mention that the most frequent values of R, Rfree and DeltaR
(that is asked about) are given in our work published in 2009 in Acta Cryst.,
D65, 1283-1291. Interestingly, they are pra
41 matches
Mail list logo
