Re: [ccp4bb] Overall forces in crystals?

James Isn't this also related to the speed of sound in the material? I guess measurements are made all made with crystals at room temperature and would be different at 100K. Any info on this for protein crystals? Speed of sound depends on density and elastic modulus though I guess would rapidl

Re: [ccp4bb] sharp beam focus and radiation damage?

Richard A paper from some time back which describes this is Increased resolution data from a large unit cell crystal collected at a third-generation synchrotron X-ray source Authors: W R Wikoff, W Schildkamp, J E Johnson Acta crystallographica. Section D, 56(Pt 7):890-3. By focusing the bending m

Re: [ccp4bb] How small is a microbeam?

Hi Yes good data with a micron size beam but, in this case, the path length was 20- 30 micron. I presume one would like a complete data set rather than a single or a few processable images. If the latter, then in principle anything is possible provided background is minimised and a low dose approa

Re: [ccp4bb] correlation length - reloaded

o unit cells be before the integrated spot intensities are given by |F_A|^2+|F_B|^2 instead of 0.5*|F_A+F_B|^2? ______ I am going to insist that the answer to this question has everything to do

Re: [ccp4bb] X-ray photon correlation length

"I'm not sure where this rumor got started that the intensity reflected from a mosaic block or otherwise perfect lattice is proportional to the square of the number of unit cells" Of course it is proportional to the square of the number of unit cells. With more cells, more photons are scattered.

Re: [ccp4bb] X-ray photon correlation length

ce length from synchrotron sources is generally larger than the x-ray path through a protein crystal. But I have not gone through the exercise of plugging in specific storage ring energies and undulator parameters to confirm this impression. Perhaps James Holton will chime in again? Ethan

Re: [ccp4bb] X-ray photon correlation length

Bernard I guess this came from "Aren't detwinning methods appropriate only in the case of true twin domains which are larger than the X-ray photon correlation length in order for the assumption to be valid that |F|^2 from each domain can be summed? This wouldn't give rise to the apparent 'diffuse s

Re: [ccp4bb] small lines in diffraction pattern

Hi Nice of Jacob to mention the paper below but I don't think it is relevant to these patterns (well it might not be relevant to anything!). I think James has given the most likely explanation. The AB type stacking disorder he mentioned is similar to the type in the paper I referenced. I think Jam

Re: [ccp4bb] small lines in diffraction pattern

Jacob Traditional mosaic spread (ordered mosaic blocks imperfectly aligned with respect to one another) gives spherical caps in reciprocal space. These would appear as arcs on a single crystal rotation photograph. If anisotropic, the arcs would be more extensive in some directions. The pattern

Re: [ccp4bb] small lines in diffraction pattern

Margriet This looks like stacking or shift disorder which can occur when perfect 3 dimensional order breaks down. For example one can have a situation where the lattice is preserved in 2 dimensions but the planes can slide with respect to one another destroying the order in the 3rd dimension, there

Re: [ccp4bb] Crystallogrphy today

Yes - reading early articles is always illuminating. Over the past few years I have looked at Charles Galton Darwin's (yes a relation) 1914 paper and Arthur Compton's in order to understand what is really happens to these x-rays. However, as Bayes work is being highlighted, I can't resist giving so

Re: [ccp4bb] is it Ok to freeze

Harry Can you clarify why you get "a substantially better structure at cryo temperatures" e.g higher intensity at high resolution due to reduction in B factors, reduction in radiation damage, anything else? Colin -Original Message- From: CCP4 bulletin board [mailto:[EMA

Re: [ccp4bb] Structural importance of ordered water?

Richard Not sure about chains but mutual hydrogen bonded networks (you mention networks) between protein, water (and ligand) surely occur. I think most self respecting waters would try and form more then two hydrogen bonds (rather then just be part of a chain) though one might not see all the (per

Re: [ccp4bb] Primary literature for cyrocooling to mitigate radiation damage

Andy I guess it all depends on what temperature you mean by cryocooling. I was not aware at the Low et. al. paper - interesting early work. Low et. al. did not study reduction in radiation damage below -130C as they noticed a large increase in mosaicity occurring so abandoned this method. They did

Re: [ccp4bb] Negative density around C of COO-

Hi Just for completeness (seeing as we are discussing scattering factors and radiation damage) there is an increased susceptibility to primary damage for sulphur due to the increased absorption which follows f'', tabulated for example in http://henke.lbl.gov/optical_constants/asf.html. The x-ray a

Re: [ccp4bb] anomalous signal of Mn and Ca ions

Dear all If you simply want to see if Ca and Mn are in your sample, you could also use x-ray fluorescence excited by the x-rays on the beamline used to collect the diffraction data. It doesn't need the energy set to be at each absorption edge, it just has to be above the edges. One then sets the fl

[ccp4bb] Jan 31st Registration Deadline for Workshop on X-ray Radiation Damage to Biological Crystalline Samples:

Fifth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples: Registration and Abstract submission will close on the 31st January 2008 at: http://user.web.psi.ch/rd5/ for the Fifth International Workshop on X-ray Radiation Damage to B

Re: [ccp4bb] bond lengths, angles, ideality and refinements

The latest Acta D shows the "social consensus" is sometimes lacking even (or especially) among very experienced and able crystallographers. Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values Ian J. Tic

[ccp4bb] Registration and Abstract submission for Fifth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples

Fifth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples : Registration and Abstract submission is now open at: http://user.web.psi.ch/rd5/ for the Fifth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples which will be held at th

Re: [ccp4bb] To bathe or not to bathe.

Richard I think the sharp spot is just small angle scattering (e.g. from domain boundaries) resulting from the beam hitting one of the defining apertures in your collimation system. If you ray trace the beam from the last defining aperture, through the guard aperture then to the detector you should

Re: [ccp4bb] To bathe or not to bathe.

Note the density of air is approximately 1000 times less than a protein crystal. The total scatter for a beam going through a 50 micron thick crystal will be similar to that from 50mm air. Most beamlines will have a path length less than this but nevertheless the air scatter will be significant w

Re: [ccp4bb] To bathe or not to bathe.

To bathers and non bathers This is an interesting discussion with several relevant points. I agree that, if small beams can pick up the best bits of the crystal that is a very good reason for using them. The background arguments can be relevant and having the beam size at the detector matched to

[ccp4bb] Workshop Announcement - X-ray Radiation Damage to Biological Crystalline Samples

The Fifth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples will be held at the Swiss Light Source from 13:00 March 3rd to 13:00 March 5th 2008. This series of workshops was originally concerned with the effects of radiation damage during investigation of protein s

Re: [ccp4bb] Questions about diffraction

Good summary as expected from James. "Have you ever heard of photon-photon scattering?" Well yes! See for example http://2physics.blogspot.com/2006/03/photon-photon-scattering.html which says "according to Quantum Electrodynamics (QED), particles can still be created in this emptiness of vacuum th

Re: [ccp4bb] Conservation of momentum - was "Is anomalous signal a different wavelength?"

Apologies for the late posting (been away). Interesting question from James and an interesting answer from Ian! There should be a radiation pressure effect here resulting in a transfer of energy and momentum to the sample. The effect is very small (the term includes flux density divided by spee

Re: [ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)

Seems to be a general issue. Read the editorial in Nature 10 May 2007 Volume 447 Number 7141, pp116. "Under the microscope - The use of 'black box' techniques carries risks." Colin -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Flip Hoedemaeker Sent: 10 May

[ccp4bb] FW: [ccp4bb] image plate shadow

Alejandro, As others have said, the most likely explanation is the attenuation of the air scatter by the sample holder. There is no sharp edge to the shadow which indicates the source of scatter is along an extended path. Ed Berry pointed out that he didn't see spots in the shadow. This might be