> If all cells are completely unsynchronized, then the occupancy-weighted > average electron density map of all the conformers will fully explain > the background-subtracted spot intensities, but if there is > cell-to-cell synchronization: it won't!
This is not correct: as I tried to explain in a previous posting, the 'optic' mode DS component which arises from what I would call 'short to medium range' correlated displacements (that is correlations due to rigid side-chain motions, or of secondary-structure units, individual helices say, or of whole domains within the same molecule, or of different molecules within the same unit cell), give rise to a non-uniform DS distribution over the *whole* diffraction pattern. You can't assume that the contributions of the optic DS at the Bragg positions are zero just because they can't be measured! From the DS equation there's absolutely no reason why the DS should be anything other than non-uniform at the Bragg position as anywhere else. Since it's equally non-uniform over the whole pattern, including at and around the Bragg positions, a planar background correction can't possibly remove it from the integrated Bragg intensities. So it's simply not correct to say that the mean electron density explains all the intensity at the Bragg positions. There will be a residual I(diffuse) = I(coherent) - I(Bragg) which is everywhere positive, as I demonstrated. I agree with you that what I would call 'long-range' correlations between different unit cells contribute largely to the 'acoustic' mode DS which is centred largely *at* the Bragg peaks. You say 'if' the cells are completely unsynchronised, but that's a big 'if' - certainly you can't simply assume that it's true. On another point you said you wanted an 'operational' definition of I(Bragg). I'm not entirely clear what you mean by that. Are you saying that you want I(Bragg) to be the total background-subtracted integrated intensity under the peak at the Bragg position, i.e. what I'm calling I(coherent). If so then it can't be the contribution from the mean density at the same time! - seems to me that's what everyone means by I(Bragg) (including you I thought!) so changing the definition will cause total confusion! Cheers -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
