Re: [ccp4bb] shadow at the edge

Abhishek The fun thing to do in these circumstances is to move the detector a known distance and see how much a point on the shadow expands (or contracts) from the centre of the detector. One can then ray trace (a simple diagram) to find the position of the object creating the shadow. In your

Re: [ccp4bb] Helium-Temp Cryo-Cooling

Jacob Good question. One case I know is for a metalloprotein where the photoreduction of the metal centre is decreased significantly at 40K compared with 110K. Acta Cryst. (2007). D63, 951-960

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon Process; was RE: [ccp4bb] Twinning Question

t; > > > > > > Of course this is trying to give some physical description for the > > electromagnetic field when I was complaining about a similar thing for > > quantum mechanics. A nice article by Freeman Dyson illustrates the > > difficulty of doing this for both approac

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon Process; was RE: [ccp4bb] Twinning Question

[mailto:merr...@u.washington.edu] Sent: 04 November 2015 21:59 To: Nave, Colin (DLSLtd,RAL,LSCI) Cc: ccp4bb Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon Process; was RE: [ccp4bb] Twinning Question On Wednesday, 04 November, 2015 09:48:13 Colin Nave wrote: > Domen

Re: [ccp4bb] Basic Anomalous Scattering Theory

An account here http://www.ccp4.ac.uk/courses/proceedings/1997/j_helliwell/main.html Colin From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob [kell...@janelia.hhmi.org] Sent: 12 March 2015 17:51 To: ccp4bb Subject: Re: [ccp4bb]

Re: [ccp4bb] Absence of contact between layers in a crystal

There should be two broad types of statistical disorder, short range and long range. The latter for example could consist of two distinct populations of crystal with near identical unit cells so the spots nearly overlap in reciprocal space. If there is a layer structure, shift disorder between

Re: [ccp4bb] proton scattering by X-rays

, i.e. d=0.26A. That's far away from the wavelength 'we' use, but not too far off from the resolution limit on a Silver source (0.31A), is it? I am not sure this can be totally neglected. Am I wrong? Cheers, Tim On 02/03/2015 04:03 PM, Colin Nave wrote: Hi Tim Although my SHELX comment

Re: [ccp4bb] proton scattering by X-rays

to take this into account, but I don't know if they do. Cheers, Tim On 02/02/2015 04:03 PM, Colin Nave wrote: “As you say the proton itself is invisible to X-rays.” Not quite! The ratio of scattering between electrons and protons should go as the inverse square of the masses. Ratio of mass 1

Re: [ccp4bb] proton scattering by X-rays

“As you say the proton itself is invisible to X-rays.” Not quite! The ratio of scattering between electrons and protons should go as the inverse square of the masses. Ratio of mass 1:1860, ratio of scattering 1:3459600. A small correction but doubtless it has been incorporated in to SHELX. Colin

Re: [ccp4bb] question about powder diffraction

, Colin Nave wrote: [...] If the whole diffraction process is considered as an interference problem then the contributions are not confined to the Bragg condition. Isn't this how textbooks on crystallography usually start? Drenth, e.g. starts with the scattering from a single electron

Re: [ccp4bb] question about powder diffraction

I think Gerard has answered the original question. To introduce additional complications (do people want complications?), there is apparently an issue with the ease of getting reflections in a powder pattern. A new theory for X-ray diffraction Fewster, P. F. (2014). Acta Cryst. A70, 257-282.

Re: [ccp4bb] PDB passes 100,000 structure milestone

From James's figure, assuming perfect lossless compression, the information content of the PDB is 20GB or about 2X10**11 bits The information content of the universe has been estimated to be 2**305 bits or 10**92 bits (this might or might not be changing). The PDB is said to be growing

[ccp4bb] FW: [ccp4bb] PDB passes 100,000 structure milestone

: [ccp4bb] PDB passes 100,000 structure milestone A logarithmic plot of cumulative entries to the PDB is approximately linear and shows a growth rate of about 15% per year. That means it doubles in size about every 5 years at current growth rate. Roger Rowlett On May 15, 2014 4:23 AM, Colin Nave

Re: [ccp4bb] twinning problem ?

, actually? Is there strong evidence supporting their existence? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: Thursday, March 13, 2014 7:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] twinning problem ? Hi Zbyszek I think

Re: [ccp4bb] twinning problems ?

Hi Jacob Maybe we can get the author to repeat the study for the other usual-suspect protein crystals to find out the truth, but the score currently seems to be 1-0 in favor of cell parameter shifts versus microcrystal orientation... You don't mean me do you? The measurement you refer to was

Re: [ccp4bb] twinning problem ?

that the particular crystal studied by Colin Nave (Acta Cryst. 1998, D54: 848) is atypical case. I processed myself hundreds of tetragonal lysozyme data sets acquired on crystals grown and mounted by various people, so I believe that my experience defines better a typical case. The second reference

Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?

] On Behalf Of Colin Nave Sent: 15 May 2013 22:17 To: ccp4bb Subject: Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity? Times up! The 3rd case I had in mind was the presence of anisotropy of the anomalous scattering in the presence of a polarised beam. John Helliwell and Pete Dunten

Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?

Oh – I seemed to have diverted Frank’s thread. Fortunately most languages themselves are highly redundant, with following characters and words being quite predictable. The entropy and redundancy of English language was analysed by Shannon (with the help of his wife) and he obtained figures of

Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?

. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 15 May 2013 10:21 To: ccp4bb Subject: Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity? Oh – I seemed to have diverted Frank’s thread. Fortunately most languages

Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?

Yes, a good summary. The use of the term redundancy (real or otherwise!) in crystallography is potentially misleading as the normal usages means superfluous/ surplus to requirements. The closest usage I can find from elsewhere is in information theory where it is applied for purposes of error

Re: [ccp4bb] popular piece on X-ray crystallography

James's original rather short comment about Debye's key observation in 1915 was clearly casting in to the CCP4BB fish pond to see who would bite. I guess I was that fish. There seems to be some confusion over dates (1914 or 1915) but this is not important. I agree that determining the size of

Re: [ccp4bb] popular piece on X-ray crystallography

Orbitals - Region of space where the probability of finding an electron is maximised Quite a key difference really in the context of determinism! Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 21 April 2013 14:38

Re: [ccp4bb] popular piece on X-ray crystallography

James In 1915, I thought Debye and Scherrer were testing for interference between the electrons in different orbits within atoms. This was in order to test the Bohr model. They got rings but they were powder diffraction rings. The method never did identify planetary type orbitals. However

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

One issue is whether the extra data for the 80% solvent volume consists of independent measurements. The references below suggest that the required oversampling of intensities is given when one has a 50% solvent volume. J. Miao, D. Sayre, and H. N. Chapman, Phase retrieval from the magnitude

Re: [ccp4bb] first use of synchrotron radiation in PX

Yes, this is a key paper demonstrating the possibilities. The answer to the question of first structure solved is a bit more difficult. Much of the early use of synchrotrons was for collecting high resolution data for refinement to supplement data collected on lab sources. This included data

Re: [ccp4bb] first use of synchrotron radiation in PX

The work at Hamburg was on insect flight muscle. It is usually quoted as the first x-ray diffraction using a synchrotron. The work is acknowledged as pioneering in John Helliwell's book. Of course the first data collection on a synchrotron was much earlier. A good account can be found here

Re: [ccp4bb] protein crystals or salt crystals

Journal of Crystal Growth 232 (2001) 498-501 and references therein Available at http://pages.physics.cornell.edu/~rthorne/publications/caylorjcg01.pdf Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: 08 February 2013 14:57 To: ccp4bb Subject: Re:

Re: [ccp4bb] PNAS on fraud

This is worth looking at as well. Suggests most papers should be retracted! http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 17:55 To: ccp4bb Subject: Re:

Re: [ccp4bb] Nobel Prize 2012

Perhaps a more complete list (now not up to date!) for crystallography can be found at http://www.iucr.org/people/nobel-prize I note however that the ebi chart is for structural biology related prizes. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]

Re: [ccp4bb] saxs on xtals

Anna Are the nanoparticles expected to be single crystals? Magnetite has Fd3m space group with a 8.4A lattice (just looked it up). This should give some diffraction features such as broad spots (broadened because of the small particle size) or rings (if there is no alignment between the

Re: [ccp4bb] saxs on xtals

superimposed? There seem to be some really bright spots which are outliers, and maybe multiple lattices. JPK On Tue, May 8, 2012 at 12:21 PM, Colin Nave colin.n...@diamond.ac.ukmailto:colin.n...@diamond.ac.uk wrote: Anna Yes, you have understood the suggestion. Could be the 220 and 311 reflections

Re: [ccp4bb] saxs on xtals

Anna Interesting. Yes, the cryo-em might be the way to go to see if some structures (i.e. not just spheres) within the protein shell are aligned. The SAXS study does make some sense. If the magnetic particles have some alignment this should manifest itself in the SAXS pattern, with the

Re: [ccp4bb] choice of wavelength

Bart Diffracted intensity goes up by the cube of the wavelength, but so does absorption and I don't know exactly about radiation damage. I think this statement should be As an approximation, diffracted intensity (integrated) goes up by the square of the wavelength, but so does absorbed

Re: [ccp4bb] MAD

Good description from Ian complemented by an amusing aside from Peter. One small point. Ian says The answer is that it turns out that the equation ('Kramer-Kronig relationship') governing X-ray scattering is completely analogous to that governing optical dispersion, Analogous implies the

Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

Dale If you could measure the continuous function you can directly calculate the electron density - there is no phase problem. The paper I referred to earlier gives the details. I don't think it is quite that easy. The paper you referred to (Miao, et al, Annu. Rev. Phys. Chem. 2008,

Re: [ccp4bb] Sub-angstrom resolution

, Am 10.01.12 18:08, schrieb Colin Nave: snip 3. The structure factors are lower for large unit cells. This will mean they will be harder to detect, particularly if there is a high background. /snip But aren't the total structure factors of a unit cell the sum of the atomic structure factors

Re: [ccp4bb] Sub-angstrom resolution

Yes, I think Ed's analysis is a bit misleading. If, as an extreme case, you have just two unit cells (in each dimension) with 300A cell dimensions, the interference function could still manifest itself out to 1A resolution. Play around with some of James Holton's simulation programs to find

Re: [ccp4bb] Sub-angstrom resolution

Message- From: Ed Pozharski [mailto:epozh...@umaryland.edu] Sent: 10 January 2012 16:09 To: Nave, Colin (DLSLtd,RAL,DIA) Cc: ccp4bb Subject: Re: [ccp4bb] Sub-angstrom resolution On Tue, 2012-01-10 at 09:04 +, Colin Nave wrote: Yes, I think Ed's analysis is a bit misleading. I apologize if I

Re: [ccp4bb] dark progression of radiation damage

Regarding striking distances, there might be some shorter range effects with low energy Auger electrons but for all practical purposes I agree with James. The main reason for this message is to ensure the original question raised by James is not forgotten as it is definitely worth resolving.

Re: [ccp4bb] To archive or not to archive, that's the question!

as well! Btw - Colin Nave wrote: (in increasing order of influence/power do we have the Pope, US president, the Bond Market and finally Gerard K?) I'm a tad disappointed to be only in fourth place, Colin! What has the Pope ever done for crystallography? --Gerard

Re: [ccp4bb] IUCr committees, depositing images

to introduce a new field for one or more TARDIS ids in a PDB deposition? It would be optional at the first, but no doubt required in the future. -James Holton MAD Scientist On 10/26/2011 4:20 PM, Colin Nave wrote: Dear Gerard Yes, perhaps I was getting a bit carried away

[ccp4bb] Continuous/shutterless readout detectors - preserving the information content. Was IUCr committees, depositing images

www.xtal.iqfr.csic.es Telf.: +34 917459550 Consejo Superior de Investigaciones Cient ficas Spanish National Research Council www.csic.es -Mensaje original- De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] En nombre de Colin Nave Enviado el: jueves, 27 de

Re: [ccp4bb] IUCr committees, depositing images

I have been nominated by the IUCr synchrotron commission (thanks colleagues!) to represent them for this issue. However, at the moment, this is a personal view. 1. For archiving raw diffraction image data for structures in the PDB, it should be the responsibility of the worldwide PDB. They are

Re: [ccp4bb] IUCr committees, depositing images

Dear George, Martin I don't understand the point that one is throwing away information by storing in frames. If the frames have sufficiently fine intervals (given by some sampling theorem consideration) I can't see how one loses information. Can one of you explain? Thanks Colin

Re: [ccp4bb] IUCr committees, depositing images

to this crucial discussion (and hence, potentially, to the community) by belittling the importance and urgency of the task. With best wishes, Gerard (B.) -- On Wed, Oct 26, 2011 at 07:58:51PM +, Colin Nave wrote: I have been nominated by the IUCr synchrotron commission (thanks

Re: [ccp4bb] Another paper structure retracted

Well this article seems to have been refereed to 11 times so presumably these 11 publications also have to be retracted. I haven't checked the number of citations for each of the 11 publications but articles citing these will also be in doubt. And then .. It reminds me somewhat of the

Re: [ccp4bb] How to evaluate Fourier transform ripples

Dear Thierry (and others) Perhaps a bit confusing to say a sharp feature such as an heavy atom. Heavy atoms are, well, heavy (lots of electrons) rather than sharp. Any ripples around them in a Fourier truncated map could swamp the lighter atoms nearby. If Zbyszek's criteria A (and his other

Re: [ccp4bb] Lattice sampling and resolution - a seeming paradox?

Dirk Another way of looking at it See slide 7 in http://www.aps.anl.gov/Science/Future/Workshops/Frontier_Science_Using_Soft_Xrays/Presentations/WeierstalTalk.pdf sampling interval 1/W (Bragg sampling) is Shannon sampling if complex Fraunhofer wavefield of object with width W is recorded. If

Re: [ccp4bb] Femtosecond Electron Beam

Jacob Very good question. People are considering this sort of thing. See for example http://www-spires.slac.stanford.edu/cgi-wrap/getdoc/slac-pub-12162.pdf Due to coulomb explosion one normally needs MeV beams to get the short bunch length. MeV beams also give a more reasonable penetration

Re: [ccp4bb] Femtosecond Electron Beam

this for sure. Sincerely, Petr From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Colin Nave [colin.n...@diamond.ac.uk] Sent: Thursday, April 14, 2011 16:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam

Re: [ccp4bb] Femtosecond Electron Beam

, magazines, is a mystery to me. Petr On Apr 14, 2011, at 9:11 PM, Colin Nave wrote: Petr has provided the Eindhoven links. For more details on fast electron imaging (as opposed to diffraction) see https://e-reports-ext.llnl.gov/pdf/343044.pdf Apparently stochastic scattering

Re: [ccp4bb] Femtosecond Electron Beam

molecule. Best, Petr On Apr 14, 2011, at 11:13 PM, Colin Nave wrote: Petr Yes, I saw the figure. Similar ones appear in the Hastings et. al. paper (the SLAC one I referenced). They use a much higher energy beam to get the short pulse length. I still believe the issues are 1

Re: [ccp4bb] **Possible spam**Re: [ccp4bb] FW: [ccp4bb] diffraction of spherulites

% seems pretty benign, unless the trays or screens have been sitting around for quite a while... JPK On Wed, Apr 6, 2011 at 12:04 PM, Colin Nave colin.n...@diamond.ac.uk wrote: Stefan Could the low angle reflections be from lamellar liquid crystals of the PEG (or a mixed PEG/water

[ccp4bb] diffraction of spherulites

I should point out that the reference I gave is quite misleading as the samples studied contained lecithin Apologies Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 06 April 2011 18:33 To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Freezing crystals in a contained system

Becky Do you have the nitrogen stream co-linear with the capillaries, with the specimen near the capillary end and therefore near the nitrogen stream exit? This might help to minimise turbulence - though nowadays other bits of kit fight to occupy this space. Regards Colin -Original

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

James All great stuff. Ø The individual crystals were not twinned (or at least I would be VERY surprised if they were) Can this be tested? The spots should show fringes around them corresponding to the shape transform of the nano-crystal. If twinned, the intensities of the fringes

Re: [ccp4bb] Why 0.1% bandwidth?

Andre The 0.1% bandwidth is a standard for flux/mrad/bandwidth or brightness (flux/mrad^2/mm^2/bandwidth) from the synchrotron source. It is an emittance rather than an acceptance. A typical perfect crystal monochromator might take (i.e. accept) a tenth of this. However, dependent on the range of

Re: [ccp4bb] Why 0.1% bandwidth?

. Technical (John's statement) or confusing (mine). Take your pick! Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 09 February 2011 14:35 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Why 0.1% bandwidth? Andre The 0.1% bandwidth is a standard

Re: [ccp4bb] Why 0.1% bandwidth?

@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 09 February 2011 15:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Why 0.1% bandwidth? Andre I should have replaced flux in my email by photons/sec to be clear (or at least a bit clearer). Flux in magnetism is the strength of the magnetic field per

Re: [ccp4bb] Why 0.1% bandwidth?

By That's I presume Bob means the 0.01% bandwidth figure is approximately the intrinsic bandwidth of a Si (111) monochromator. The 0.1% bandwidth in the title of the email is the standard bandwidth often used to define the output of synchrotron sources. When defining flux within a certain

Re: [ccp4bb] Merging data to increase multiplicity

Can people say how high mosaicity is defined. High relative to what? Is it high relative to the rotation range for each image, high relative to the incident beam divergence, high relative to the (angular) detector resolution or something else? Regards Colin From: CCP4 bulletin board

[ccp4bb] FW: [ccp4bb] Merging data to increase multiplicity

range. I hope this answers your question, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: Friday, January 28, 2011 3:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

I too think the phrase super-resolution is rather misleading, in particular the analogy with light microscopy methods. Super-resolution in these latter cases is achieved via different physical phenomena (think excitations not waves). Would one claim super-resolution when refining the

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distanceaccuracies

reservations about some uses of creative language. With best wishes, Gerard. -- On Thu, Jan 06, 2011 at 11:13:41AM -, Colin Nave wrote: I too think the phrase super-resolution is rather misleading, in particular the analogy with light microscopy methods. Super

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Does one regard the metal atom in a metalloprotein as being part of the protein? If so, a shared metal could occupy a special position in a dimer for example. In Acta Cryst. (2008). D64, 257-263 Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid

Re: [ccp4bb] unusual diffraction spots

Dear all Herman might be correct in this case but spot shapes can be affected by imperfactions in the crystal rather than the crystal shape. Some types of imperfections (e.g. strain) manifest themselves more for higher resolution data. They are still there for the low resolution data, but buried

Re: [ccp4bb] Strange spots

resolution in an anti-clockwise manner.but I am still digesting your movie Behind the scenes discussion, between Colin Nave, James Holton and myself, has been going on. Since Colin has been the main leader in these I leave it to Colin to take it up from here and I can chip

Re: [ccp4bb] Strange spots

The detector issue could be resolved by moving it to a different distance and recording the pattern again. In the absence of further info, my vote goes for James Holton's explanation - the effect could be due to optocal misaligenment Colin -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] Help with model bias in merihedral twin + Refmac5

Peter Yes, by 2Fo-Fc type maps I was including the weighted maps you mention (which should be better). The main issue is whether 3mF(obs)-2DF(calc) and higher coefficients would be better for the twinned reflections Regards Colin From: CCP4 bulletin

Re: [ccp4bb] Merohedral twining for P212121. -

Matheus, Ian, Frank, Jonathan Thanks for all the comments. It is easy to calculate the amount of splitting of the spots once the cell dimensions of each component are known. For the P212121 case, with a-b twinning, splitting will be zero in the c* direction. The splitting will increase as h and k

Re: [ccp4bb] Merohedral twining for P212121.

Matheus A couple of points Firstly, isn't this pseudo merohedral rather than merohedral. I realise you didn't mention either in your email but it is in the title of the previous message. Secondly, the difference in the cell dimensions (b=123.92 and c=128.89A) appears to be quite large and

Re: [ccp4bb] Merohedral twining for P212121. -

comments appreciated. Cheers Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: 22 June 2010 17:35 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Merohedral twining for P212121. On Tue, Jun 22, 2010 at 4:32 PM, Colin Nave

Re: [ccp4bb] Help with Bayes's theorem

This is quite a good one as well http://www.inference.phy.cam.ac.uk/mackay/pope.html I recall the pope analysis followed on from a Nature article covering the O J Simpson example (also covered in the NY times link). Sean Eddy who is an author on the above link wrote what I regard as an

Re: [ccp4bb] Refining against images instead of only reflections

John, Ethan Some good points being made regarding the discrepancy between TLS models and measured diffuse scatter. However, as James has pointed out, measuring the diffuse scatter is not that easy due to the contribution of the lattice This could be why there are some problems as large motions

Re: [ccp4bb] Refining against images instead of only reflections

Holton MAD Scientist Colin Nave wrote: Nice overview from Ian - though I think James did make some good points too. I thought it might be helpful to categorise the various contributions to an imperfect diffraction

Re: [ccp4bb] Refining against images instead of only reflections

Biology, WHRI, School of Medicine, Cardiff University, Heath Park, CF14 4XN email: rizkall...@cf.ac.uk phone + 44 29 2074 2248 Colin Nave colin.n...@diamond.ac.uk 23/01/10 11:35 PM Nice overview from Ian - though I think James did make some good points too. I thought it might

Re: [ccp4bb] Refining against images instead of only reflections

Nice overview from Ian - though I think James did make some good points too. I thought it might be helpful to categorise the various contributions to an imperfect diffraction pattern. Categorising things seems to be one of the English (as distinct from Scottish, Irish or Welsh!) diseases. 1.

Re: [ccp4bb] Refining against images instead of only reflections

James Some comments! The diffuse scatter does NOT tell you about the deviations from this average; it tells you how the deviations are correlated from unit cell to unit cell. Does this just refer to the scatter near the Bragg peaks? If there is no correlation from unit cell to unit cell

[ccp4bb] FW: [ccp4bb] Refining against images instead of only reflections

Jacob Yes, discussions have taken place but perhaps more private than on the CCP4 bulleting board! So I am glad someone has raised the issue. The present approximation that people make works very well in the majority of cases. The approximation is implied during the integration of a spot and is

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures

For previous debate on this issue see (in CCP4 archives) https://www.jiscmail.ac.uk/cgi-bin/webadmin?S2=CCP4BBq=s=The+importanc e+of+USING+our+validation+toolsf=a=b= I think Eleanor started it https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708L=CCP4BBP=R75676 And of course it is deja vu

Re: [ccp4bb] decrease of background with distance?

John Another point which might resolve some of the confusion regarding detector distances (or add to the confusion) that moving the detector back was not the setting required but a small collimator (0.2mm) and slitting down the divergence to control the spot size versus the broader halo of

Re: [ccp4bb] decrease of background with distance?

Dear John By inelastic I guess you mean the acoustic scattering? In case people are worried, the change in energy of the x-ray during this interaction is very small. Have you any views on the correct treatment for the halo corresponding to the acoustic scatter (or perhaps for the static case

Re: [ccp4bb] decrease of background with distance?

Ian Maybe - maybe not. Investigations of acoustic and optical components of diffuse scatter from proteins were carried out in the 80s and 90s including of course work at Birkbeck (which I am sure you are aware of) Refs can be found in Glover et. al. Acta Cryst. (1991). B47, 960-968. This paper

Re: [ccp4bb] decrease of background with distance?

Ian Surely the Bragg peaks, acoustic and optic components of the diffuse scatter all occupy a finite volume in reciprocal space. In x-ray scattering/diffraction the area they occupy on a detector therefore expands as the detector is moved further away. However, one will not always see this. If the

Re: [ccp4bb] decrease of background with distance?

of the detector constant has absolutely NO effect on the photons/spot from Bragg vs diffuse scattering. It took me a while to become convinced of this, and I still owe Colin Nave a few beers as a result. Nevertheless, the experimental evidence was given by Gonzalez, Denny Nave in 1994. HTH -James Holton MAD

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about - biochemistry to validate model

Sorry, they can be validated to some extend using biochemical data! You are joking, right? Perhaps a distinction has to be made between model validation and making useful predictions from the model. Something like Model Validation - testing model against data. In case of protein crystallography

Re: [ccp4bb] crystallography teaching advice: f(S) ?

Interesting discussion by authoritative and expert CCP4BB contributors. Francis Bacon is often cited as one of the originators of enlightenment science. An recent (1964!) update on his methods can be found in http://pages.cs.wisc.edu/~markhill/science64_strong_inference.pdf. I think this