[ccp4bb] NMR review
Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA ⁄ RNA molecule that are flexible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the final electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain?
Re: [ccp4bb] NMR review
Dear Bernhard, Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.): Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA ⁄ RNA molecule that are flexible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the final electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) That doesn't sound wrong to me: the flexible parts are at different relative positions in the unit cells and thus their partial-structure scattering waves do not have a constant phase relation to each other, i.e., they don't give a coherent contribution to the total scattering. But I don't agree to their conclusion, since disorder doesn't necessarily mean, that there won't be any interpretable electron density left. The floppy parts could still be interpreted at an effective lower resolution and thus will not be ignored. Maybe the authors were annoyed by a vanishing NMR signal because the macromolecule crystallized in the NMR test tube ;-) Best regards, Dirk. Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain? -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] NMR review
Does out of phase imply incoherent scattering? I though it means inelastic Compton scattering? -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Thursday, January 12, 2012 1:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] NMR review Dear Bernhard, Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.): Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA / RNA molecule that are ?exible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the ?nal electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) That doesn't sound wrong to me: the flexible parts are at different relative positions in the unit cells and thus their partial-structure scattering waves do not have a constant phase relation to each other, i.e., they don't give a coherent contribution to the total scattering. But I don't agree to their conclusion, since disorder doesn't necessarily mean, that there won't be any interpretable electron density left. The floppy parts could still be interpreted at an effective lower resolution and thus will not be ignored. Maybe the authors were annoyed by a vanishing NMR signal because the macromolecule crystallized in the NMR test tube ;-) Best regards, Dirk. Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain? -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universit t M nchen Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] NMR review
On 12 January 2012 09:57, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: That doesn't sound wrong to me: the flexible parts are at different relative positions in the unit cells and thus their partial-structure scattering waves do not have a constant phase relation to each other, i.e., they don't give a coherent contribution to the total scattering. From http://scienceworld.wolfram.com/physics/IncoherentScattering.html : Scattering for which reemission occurs by a cascade process, so the frequency of emission is not the same as that of the incident. . We don't see any change of frequency (or wavelength) in the majority of the scattering from disordered regions so it's Rayleigh (coherent) scattering. There will be a small amount of Compton (incoherent) scattering resulting from the ionisation events which are responsible for radiation damage but hopefully freezing will keep this to a minimum. Cheers -- Ian
Re: [ccp4bb] NMR review
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Bernhard, without ever having looked at an NMR experiment, intuitively the resolution of an NMR experiment should be given as the magnitude of the minimal chemical shift that could be observed/distinguished. Beware that 'resolution' does not necessarily mean 'optical resolution', and the fact that we provide the resolution of diffraction experiments in Angstrom can surely be confusing, as well. 1/Angstrom, as often cited in charge density studies, much better reflects that 'resolution' of a data set refers to the scattering angle at which there were still spots on the detector. Concerning your quote: even scientists are not free of emotions even though sometimes one might get the impression that some pretend they were, which inevitably leads to tensions that might be released in phrases like your quote... Cheers, Tim On 01/12/2012 10:30 AM, Bernhard Rupp (Hofkristallrat a.D.) wrote: Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA ⁄ RNA molecule that are flexible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the final electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain? - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPDrboUxlJ7aRr7hoRAqGJAKCRq3y9yeSLiy+e3P3Se9XqDVBLwQCeM921 vt5ADacDA81CNw0us7k+gL8= =VN3V -END PGP SIGNATURE-
Re: [ccp4bb] NMR review
My understanding of coherence is a constant phase relation between waves. Of course, this breaks down for inelastic scattering, but (in)coherence can also be described without any change in wavelength. Best regards, Dirk. Am 12.01.12 11:27, schrieb Bernhard Rupp (Hofkristallrat a.D.): Does out of phase imply incoherent scattering? I though it means inelastic Compton scattering? -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Thursday, January 12, 2012 1:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] NMR review Dear Bernhard, Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.): Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA / RNA molecule that are ?exible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the ?nal electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) That doesn't sound wrong to me: the flexible parts are at different relative positions in the unit cells and thus their partial-structure scattering waves do not have a constant phase relation to each other, i.e., they don't give a coherent contribution to the total scattering. But I don't agree to their conclusion, since disorder doesn't necessarily mean, that there won't be any interpretable electron density left. The floppy parts could still be interpreted at an effective lower resolution and thus will not be ignored. Maybe the authors were annoyed by a vanishing NMR signal because the macromolecule crystallized in the NMR test tube ;-) Best regards, Dirk. Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain? -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] NMR review
We don't see any change of frequency (or wavelength) in the majority of the scattering from disordered regions so it's Rayleigh (coherent) scattering. There will be a small amount of Compton (incoherent) scattering resulting from the ionisation events which are responsible for radiation damage but hopefully freezing will keep this to a minimum. Sorry just re-read that realised the bit about freezing is not quite what I meant! Freezing will not of course reduce the amount of incoherent scattering in the least. It may however alleviate its effects (which is what I meant). Cheers -- Ian
Re: [ccp4bb] NMR review
On 12 January 2012 10:33, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: My understanding of coherence is a constant phase relation between waves. Correct. For a perfect crystal all the unit cells are identical so they scatter in phase and this gives rise to the interference effect we see as Bragg spots, as you say arising from a constant phase relation in specific directions. For a disordered crystal the unit cells are not the same: this destroys the interference effect but there's still a constant phase relation in any specified direction so it's still coherent. Of course, this breaks down for inelastic scattering, but (in)coherence can also be described without any change in wavelength. That's not the definition of incoherence used by the physicists. Of course you're free to redefine it but I think that just confuses everyone. Cheers -- IAn
Re: [ccp4bb] NMR review
I'm not a physicist - but isn't (in)coherence also used to describe the property of sources of electromagnetic waves with constant wavelength? For instance, an incoherent sodium vapour light source (only looking at one emission band) compared to a coherent Laser, or the incoherent emission from a conventional X-ray source or an X-ray undulator compared to a Free-electron-X-ray-Laser? If yes, then we could describe diffraction from a crystal in a similar way by treating the crystal as a light-source, both with coherent and incoherent scattering from the well-ordered and disordered parts, respectively, without any need to change the wavelength. In this analogy, the ordered part would have the coherence of a Laser, whereas the disordered part would have the incoherence of a vapour lamp. Best regards, Dirk. Am 12.01.12 11:57, schrieb Ian Tickle: On 12 January 2012 10:33, Dirk Kostrewakostr...@genzentrum.lmu.de wrote: My understanding of coherence is a constant phase relation between waves. Correct. For a perfect crystal all the unit cells are identical so they scatter in phase and this gives rise to the interference effect we see as Bragg spots, as you say arising from a constant phase relation in specific directions. For a disordered crystal the unit cells are not the same: this destroys the interference effect but there's still a constant phase relation in any specified direction so it's still coherent. Of course, this breaks down for inelastic scattering, but (in)coherence can also be described without any change in wavelength. That's not the definition of incoherence used by the physicists. Of course you're free to redefine it but I think that just confuses everyone. Cheers -- IAn -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] NMR review
On 12 January 2012 11:25, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: I'm not a physicist - but isn't (in)coherence also used to describe the property of sources of electromagnetic waves with constant wavelength? For instance, an incoherent sodium vapour light source (only looking at one emission band) compared to a coherent Laser, or the incoherent emission from a conventional X-ray source or an X-ray undulator compared to a Free-electron-X-ray-Laser? If yes, then we could describe diffraction from a crystal in a similar way by treating the crystal as a light-source, both with coherent and incoherent scattering from the well-ordered and disordered parts, respectively, without any need to change the wavelength. In this analogy, the ordered part would have the coherence of a Laser, whereas the disordered part would have the incoherence of a vapour lamp. I'm not a physicist either but if I look up 'coherence' in Wikipedia (not necessarily the most accurate source of information I admit!): The most monochromatic sources are usually lasers; such high monochromaticity implies long coherence lengths (up to hundreds of meters). For example, a stabilized helium-neon laser can produce light with coherence lengths in excess of 5 m. Not all lasers are monochromatic, however (e.g. for a mode-locked Ti-sapphire laser, Δλ ≈ 2 nm - 70 nm). LEDs are characterized by Δλ ≈ 50 nm, and tungsten filament lights exhibit Δλ ≈ 600 nm, so these sources have shorter coherence times than the most monochromatic lasers. ( http://en.wikipedia.org/wiki/Coherence_%28physics%29 ). So coherence is indeed directly related to monochromaticity so there's no energy dispersion on elastic scattering. Of course X-rays from any source will also have (more or less depending on the physics of X-ray production) a characteristic Δλ which implies some degree of incoherence in the incident and therefore the scattered beams. The question though is whether or not the scattering event adds to this intrinsic incoherence. When we talk about 'coherent scattering' we mean that the degree of incoherence of the scattered beam is unchanged relative to that of the incident beam. Cheers -- Ian Cheers -- Ian
Re: [ccp4bb] NMR review
I think the problem is related to the term coherence being used to describe both the type of *radiation* and the mode of *scattering*. When talking about (xray) radiation, it denotes the phase relationship between photons, and therefore even a monochromatic beam can be incoherent (whereas a polychromatic one is, of course, always incoherent). In terms of scattering, however, what matters is the self-coherence between different partial waves scatted from different unit cells. Taking things this way, the classical crystallographic diffraction experiment with a rotating anode actually makes use of coherent scattering of an incoherent beam! Cheers, Oliver PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa [kostr...@genzentrum.lmu.de] Sent: Thursday, January 12, 2012 12:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] NMR review I'm not a physicist - but isn't (in)coherence also used to describe the property of sources of electromagnetic waves with constant wavelength? For instance, an incoherent sodium vapour light source (only looking at one emission band) compared to a coherent Laser, or the incoherent emission from a conventional X-ray source or an X-ray undulator compared to a Free-electron-X-ray-Laser? If yes, then we could describe diffraction from a crystal in a similar way by treating the crystal as a light-source, both with coherent and incoherent scattering from the well-ordered and disordered parts, respectively, without any need to change the wavelength. In this analogy, the ordered part would have the coherence of a Laser, whereas the disordered part would have the incoherence of a vapour lamp. Best regards, Dirk. Am 12.01.12 11:57, schrieb Ian Tickle: On 12 January 2012 10:33, Dirk Kostrewakostr...@genzentrum.lmu.de wrote: My understanding of coherence is a constant phase relation between waves. Correct. For a perfect crystal all the unit cells are identical so they scatter in phase and this gives rise to the interference effect we see as Bragg spots, as you say arising from a constant phase relation in specific directions. For a disordered crystal the unit cells are not the same: this destroys the interference effect but there's still a constant phase relation in any specified direction so it's still coherent. Of course, this breaks down for inelastic scattering, but (in)coherence can also be described without any change in wavelength. That's not the definition of incoherence used by the physicists. Of course you're free to redefine it but I think that just confuses everyone. Cheers -- IAn -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt Kennen Sie schon unsere app? http://www.fz-juelich.de/app
Re: [ccp4bb] NMR review
On 12 January 2012 13:02, Weiergräber, Oliver H. o.h.weiergrae...@fz-juelich.de wrote: I think the problem is related to the term coherence being used to describe both the type of *radiation* and the mode of *scattering*. When talking about (xray) radiation, it denotes the phase relationship between photons, and therefore even a monochromatic beam can be incoherent (whereas a polychromatic one is, of course, always incoherent). In terms of scattering, however, what matters is the self-coherence between different partial waves scatted from different unit cells. Taking things this way, the classical crystallographic diffraction experiment with a rotating anode actually makes use of coherent scattering of an incoherent beam! I think you're right, one can consider 2 types of coherence: temporal or longitudinal coherence which is measured by the average auto-correlation function of the wave with a copy of itself displaced by some time interval, and spatial or lateral coherence which is measured by the average cross-correlation function of one part of the wave-front with another part at the same instant in time. Spatial coherence is obviously relevant to diffraction because different parts of the wave-front get scattered by different parts of the crystal, so if there's disorder it will lead to spatial decoherence (aka diffuse scattering). In scattering we are considering what happens when an X-ray photon interacts with an electron so then temporal decoherence will only occur if in an inelastic collision the photon loses some of its energy to the electron. So one must take care to distinguish (in)coherent scattering from (in)coherent diffraction. Cheers -- Ian
Re: [ccp4bb] NMR review
PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain? Dear Bernhard, As a cross-trained person, I am trying to answer your question about NMR related stuff and hopefully not create more confusion. As far as I know, the meaning of 'resolution' in NMR comes from the calculated structures (products), not from the NMR signals (experimental data) themselves. Of course, the ensemble of structures calculated from NMR are derived from the restraints obtained from the experimental data such as NOE, RDC, PRE, etc.. Thus, the 'average resolution' calculated from the ensemble of structures reflect the variations in the three-dimensional coordinate space. without ever having looked at an NMR experiment, intuitively the resolution of an NMR experiment should be given as the magnitude of the minimal chemical shift that could be observed/distinguished. Regarding Tim's comments, I think he is referring to the 'linewidths' of NMR signals. I am sure that some people could try to come up with the 'new definition of resolution' in NMR that is related to the linewidths of signals (and try to convince other people, which may be even more difficult), but the linewidths in different experiments are coming from different parameters, and I don't know how one can correlate the linewidths to the resolution... Sangwon Lee Postdoctoral Associate Yale School of Medicine
