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James, I think the problem is that your simulation just doesn't contain enough atoms in the unit cell with correlated displacements to exhibit significant optic DS, i.e. with only 1 or 2 atoms it will be dominated by Einstein-model DS which as I explained before is locally uniform and therefore can be fitted by a planar background function. Cheers -- Ian > -----Original Message----- > From: [log in to unmask] [mailto:[log in to unmask]] On > Behalf Of James Holton > Sent: 29 January 2010 09:43 > To: [log in to unmask] > Subject: Re: [ccp4bb] Refining against images instead of only reflections > > All I'm saying is that when I calculate the average general scattering > from 8192 random configurations of one disordered atom per unit cell: > http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtal_diffuse.gif > and then subtract from that the general scattering from an > "occupancy-weighted model" with the two possible atom positions are at > half occupancy: > http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtalAB_Fsum.gif > I get an difference image that shows only the smooth diffuse-scatter > background, with no spots to speak of: > http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtals_diffuse_minus_Fsu m. > gif > > But, if I calculate the average general scattering from an "all A" and > an "all B" crystal: > http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtalAB_Isum.gif > and subtract from it the same partial-occupancy model image as above: > http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtalAB_Fsum.gif > I get an image where some of the spots have been subtracted out, but > others are still quite pronounced: > http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtals_Isum_minus_Fsum.g if > > So, in the first case, the partial-occupancy model produced exactly the > same background-subtracted spot intensities as the "unsynchronized > disorder" case, but this was not so when the disorder was synchronized. > > What did I do wrong? > > As far as my "operational" definition of a "Bragg peak" (a term which > already has two definitions), I am merely suggesting that the > nearly-universal practice of subtracting the "local background" is a > very pragmatic definition of a "spot intensity". Nearly all available > data were collected in this way, and it actually is a reasonable thing > to do if the disorder from cell to cell is uncorrelated (as evidenced > above). > > However, I totally agree with you that the disorder in protein crystals > may well be correlated across large patches of unit cells. If that is > the case, then the "average occupancy model" that is all but universally > implemented by refinement programs will never be able to explain the > background-subtracted spot intensities. > > -James Holton > MAD Scientist > > > Ian Tickle wrote: > >> 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 [log in to unmask] 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. 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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