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Dear Lattice Obsessed: The issue of cell parameters has come up on ccp4bb before, and determination of accurate cell constants is a non trivial issue. First, accuracy and precision are separate things requiring different corrective approaches. Generally, a LSQ of the hkls can give you a quite precise estimate, but to obtain accurate parameters, you need internal standards or extrapolation techniques to 2theta=180, where effects like absorption, sample thickness, secondary extinction etc approach zero. I have a summary of those at http://ruppweb.dyndns.org/weblat/weblat_description.htm The option to directly measure those reflections at high thetas (eg Bond's method) is nil for proteins, and extrapolation from the poor thetas we have is equally risquee. In addition, internal standards are necessary to account for instrument, wavelength and other systematic errors that do not cancel out. Given that, temperature becomes the next issue, and if you give cell constants to 5 or 6 digits, you better know the temperature accurately. Finally, protein crystals probably show different temperature behavior than comparable isotropic small molecule/solid materials, and I would expect that to a large degree cell changes happen via displacive events at molecular contacts, and it is relatively safe to assume from physics that the bulk material does not undergo large bond length changes. Given that, the assumption made by whatcheck that the cell should be compatible with known bond restraints remains reasonable. Unfortunately, as mentioned, the remedy is unclear and I yet need to see a case where the - in principle valid - application of the deformation matrix makes a significant difference in biological interpretation. Why it is not selfconsistent and does not converge and often flips around when applied I do not quite understand. Has anyone ever iterated this to the bitter end of (non)convergence? best regards, BR -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Artem Evdokimov Sent: Tuesday, November 29, 2005 4:40 PM To: Edward Berry; CCP4BB Subject: Re: [ccp4bb]: ice lattice parameters - was: WHATCHECK Deformation Matrix - is it advisable to c orrect the cell ? *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** On the subject of calibration with crystals - In the good old days (not really all that long ago) I used to do calibrations using sucrose crystals. The advantage of the latter is that you can always find some laying around (e.g. in sugar packets near the coffee machine). Lattice parameters for sucrose can be readily obtained from e.g. the CSD. Artem
