Hi,
yes, shifts depend on resolution indeed. See pages 75-77 here:
http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf
Pavel
On Fri, Oct 14, 2011 at 7:34 PM, Ed Pozharski wrote:
> On Fri, 2011-10-14 at 23:41 +0100, Phil Evans wrote:
> > I just tried refining a "finis
Dear all,
I obtained 20 peptide models (with lowest energy) calculated by CNS program.
Now I want to make a table for structure statistics, but I don't know how to
calculate Ebond Eangle Eimproper Evdw ENOE Ecdih Etotal , r.m.s. deviation from
experimental constraints, and r.m.s. deviations fro
On Fri, 2011-10-14 at 23:41 +0100, Phil Evans wrote:
> I just tried refining a "finished" structure turning off the FreeR
> set, in Refmac, and I have to say I can barely see any difference
> between the two sets of coordinates.
The amplitude of the shift, I presume, depends on the resolution and
Each R-free flag corresponds a particular HKL index. Redundancy refers to the
number of times a reflection corresponding to a given HKL index is observed.
The final structure factor of a given HKL can be thought of as an average of
these redundant observations.
Related to your question, someone
Now it would be interesting to refine this structure to convergence,
with the original free set. If I understood correctly Ian Tickle has
done essentially this, and the Free R returns essentially to its
original value: the minimum arrived at is independent of starting
point, perhaps within limita
Dear Gerard,
I'm very happy for the discussion to be on the CCP4 list (or on the IUCR
forums, or both). I was only trying to not create too much traffic.
All the best,
Tom T
>> Dear Tom,
>>
>> I am not sure that I feel happy with your invitation that views on
>> such
>> crucial matters as
I may be missing something or someone could point out that I am wrong and why
as I am curious, but with a highly redundant dataset the difference between
refining the final model against the full dataset would be small based upon the
random selection of reflections for Rfree?
Dear Tom,
I am not sure that I feel happy with your invitation that views on such
crucial matters as these deposition issues be communicated to you off-list.
It would seem much healthier if these views were aired out within the BB.
Again!, some will say ... but the difference is that there i
For those who have strong opinions on what data should be deposited...
The IUCR is just starting a serious discussion of this subject. Two
committees, the "Data Deposition Working Group", led by John Helliwell,
and the Commission on Biological Macromolecules (chaired by Xiao-Dong Su)
are working o
I just tried refining a "finished" structure turning off the FreeR set, in
Refmac, and I have to say I can barely see any difference between the two sets
of coordinates.
From this n=1 trial, I can't see that it improves the model significantly, nor
that it ruins the model irretrievably for futu
On Friday, October 14, 2011 02:45:08 pm Ed Pozharski wrote:
> On Fri, 2011-10-14 at 13:07 -0700, Nat Echols wrote:
> >
> > The benefit of including those extra 5% of data is always minimal
>
> And so is probably the benefit of excluding when all the steps that
> require cross-validation have alr
Thanks for the clear explanation. I understood that.
But I was trying to understand how this would negatively affects the
initial model to render it useless or less useful.
In the scenario that you presented, I would expect a better result
(better model) if the initial model was refined with a
We have obligations that extend beyond simply presenting a "best" model.
In an ideal world, the PDB would accept two coordinate sets and two sets of
statistics, one for the last step where the cross-validation set was valid, and
a final model refined against all the data. Until there is a cle
On Fri, 2011-10-14 at 13:07 -0700, Nat Echols wrote:
> You should enter the statistics for the model and data that you
> actually deposit, not statistics for some other model that you might
> have had at one point but which the PDB will never see.
If you read my post carefully, you'll see that
Recently we (I mean WE - community) frequently refine structures around 1
Angstrom resolution.
This is not what for the Rfree was invented. It was invented to go away with
3.0-2.8 Angstrom data
in times when people did not possess facilities good enough to look on the
electron density maps….
W
Let's say you have two isomorphous crystals of two different
protein-ligand complexes. Same protein different ligand, same xtal
form. Conventionally you'd keep the same free set reflections (hkl
values) between the two datasets to reduce biasing. However if the
first model had been refined a
I still don't understand how a structure model refined with all data
would negatively affect the determination and/or refinement of an
isomorphous structure using a different data set (even without doing
SA first).
Quyen
On Oct 14, 2011, at 4:35 PM, Nat Echols wrote:
On Fri, Oct 14, 2011
On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang wrote:
> Sorry, I don't quite understand your reasoning for how the structure is
> rendered useless if one refined it with all data.
>
"Useless" was too strong a word (it's Friday, sorry). I guess simulated
annealing can address the model-bias issue,
Regarding refinement against all reflections: the main goal of our work is
to provide the best possible representation of the experimental data in the
form of the structure model. Once the structure building and refinement
process is finished keeping the Rfree set separate does not make sense any
m
Recent experience indicates that the PDB is checking these statistics very
closely for new depositions. The checks made by the PDB are intended to
prevent accidents and oversights made by honest people from creeping into the
database. "Getting away" with something seems to imply some intention
Sorry, I don't quite understand your reasoning for how the structure
is rendered useless if one refined it with all data.
Would your argument also apply to all the structures that were refined
before R-free existed?
Quyen
You should enter the statistics for the model and data that you
ac
Hi Ed,
> This is a follow up (or a digression) to James comparing test set to
> missing reflections. I also heard this issue mentioned before but was
> always too lazy to actually pursue it.
>
> So.
>
> The role of the test set is to prevent overfitting. Let's say I have
> the final model and
On Fri, Oct 14, 2011 at 12:52 PM, Ed Pozharski wrote:
> The second question is practical. Let's say I want to deposit the
> results of the refinement against the full dataset as my final model.
> Should I not report the Rfree and instead insert a remark explaining the
> situation? If I report th
This is a follow up (or a digression) to James comparing test set to
missing reflections. I also heard this issue mentioned before but was
always too lazy to actually pursue it.
So.
The role of the test set is to prevent overfitting. Let's say I have
the final model and I monitored the Rfree ev
Automated outlier rejection in scaling will handle a lot of things,
including ice. Works better with high multiplicity. Unless, of course,
your ice rings are "even", then any integration error due to ice will be
the same for all the symmetry mates and the scaling program will be none
the wi
On 10/11/2011 12:33 PM, Garib N Murshudov wrote:
We need better way of estimating "unobserved" reflections.
Indeed we do! Because this appears to be the sum total of how the
correctness of the structure is judged. It is easy to forget I think
that from the "point of view" of the refinement
These rings are nanocrystalline cubic ice (ice Ic, as opposed to the
"usual" ice Ih). It is an interesting substance in that noone has ever
prepared a large single crystal of it. In fact, for very small crystals
it can be hard to distinguish it from amorphous ice (or "glassy
water"). The thr
Hi all,
The Protein Data Bank in Europe (PDBe; pdbe.org) regularly produces Quips,
short stories about QUite Interesting Pdb Structures (pdbe.org/quips). Quips
address biologically interesting aspects of one or more PDB entries, coupled
with interactive graphics views and often a mini-tutorial
(Posted on behalf of wwPDB)
The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is pleased to direct PDB
depositors and users to the recommendations of the wwPDB X-ray Validation Task
Force (VTF) that were published in the journal Structure this week (2011, vol.
19: 1395-1412; http://www.cell.c
Respected Sir,
I am sorry I wrote it wrongly, its resolution-
independent X-ray weight rather. I use ccp4i
so the input for the weight is what i mentioned
previously-
"Refinement parameters- weighing term (when
auto weighing is turned off)" in refmac.
Thanking you
With Regads
M. Kavyashree
-I
> Yes, the weight mentioned in the paper was
> weight matrix, but the one i used was the
> option under "Refinement parameters- weighing
> term (when auto weighing is turned off)".
> But If I really wasnt to change the weight matrix
> where should I change (in the code?)?
No, the weights referred
Respected Sir,
Yes, the weight mentioned in the paper was
weight matrix, but the one i used was the
option under "Refinement parameters- weighing
term (when auto weighing is turned off)".
But If I really wasnt to change the weight matrix
where should I change (in the code?)?
No, I dint mean a big
> Try the GNU (compiler) and see what it says. ;)
Hi Francois - I won't bore you with the long list of compiler errors
that gfortran gives with my code (ifort compiles the identical code
without error and up until now it has worked just fine on both 32 & 64
bit machines as long as don't try to all
Hi your X-ray weight of .08 seems very small, the optimal value is
normally in the range 1 to 4 (I usually set it initially at the
median, i.e. 2.5). But which weight keyword did you use "WEIGHT
MATRIX .08" or "WEIGHT AUTO .08" (the latter is I think undocumented,
so I'm guessing the first)? Anyw
Respected Sir,
For one of the structures that I did optimisation
had values - (resolution of the data - 2.35Ang)
Before optimization- (Bfactor weight=1.0, X-ray Weight - auto)
R factor 0.2362
R free0.2924
-LLfree 7521.8
rmsBOND 0.0160
zBOND 0.660
After optimisation- (B-factor weight
On 10/14/2011 06:31 PM, Ian Tickle wrote:
Hello all, some Fortran developer out there must know the answer to
this one. I'm getting a "forrtl: severe (41): insufficient virtual
memory" error when allocating dynamic memory from a F95 program
compiled with Intel Fortran v11.1.059. The program was
Hello all, some Fortran developer out there must know the answer to
this one. I'm getting a "forrtl: severe (41): insufficient virtual
memory" error when allocating dynamic memory from a F95 program
compiled with Intel Fortran v11.1.059. The program was compiled on an
old ia-32 Linux box with 1Gb
Sorry I just re-read your last email and realised and didn't read it
properly the first time. But what I said still stands: you can of
course try to optimise the weights at an early stage (before adding
waters say), there's no harm doing that, but there's also not much
point since you'll have to d
It must be the same complete model that you refined previously, I
doubt that it will give the correct answer if you leave out the waters
for example.
You say "there was quite a difference". Could you be more specific:
what were the values of the weights, R factors and RMSZ(bonds/angles)
before an
Dear Michael,
alternative people to service FPLC systems in the UK are called LC Services
http://www.lcservs.com/ and came highly recommended to us.
cheers
charlie
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Michael
Colaneri
Sent: 12 October 2011 19:29
To: CCP4BB@
Karolinska Institutet has a vacancy for A doctoral student with doctoral grant
in Structural Immunology/Bacteriology
Department
Department of Medicine, Huddinge
Description of research group and project
Center for Infectious Medicine (CIM), Department of Medicine, Huddinge is
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Hello ,
Can any one send me pdf of this paper as its a old paper and not
accessible here .
M.F. Perutz, Preparation of haemoglobin crystals. *J. Cryst. Growth*
, * 2 * (1968), pp. 54–56.
On Fri, Oct 14, 2011 at 10:42 AM, ChenTiantian
wrote:
> Hi there,
> I am processing a data
Respected Sir,
Thank you for your clarification. I had adopted this
method recently. My doubt was if we have to optimize
these two parameters during refinement, should we have
the whole model along with water and ligands or only
protein with few water positioning is enough. The reason
why I am ask
Your main problem is not the ice rings but a wrong lattice/indexing solution. R
factors are very high for even low res shells and I/sigma very low. To me this
tells you are not finding your diffraction spots at all.
First thing to try: Take more images for the indexing step and use only the
str
Hi Kavya
The resolutions of the structures mentioned in the paper were only
examples, the Rfree/-LLfree minimisation method (which are actually
due to Axel Brunger & Gerard Bricogne respectively) does not depend on
resolution.
If the structures are already solved & refined, you don't need to do
a
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