The main reason was related to absorption. If you didn't completely bathe the crystal in the xray beam, then the diffracting volume of the crystal would be different during the data collection, and thus, scaling would be inaccurate, especially when there was radiation damage. This was especially true when you weren't sure that the crystal was well-centered in the xray beam (in a cryostat, and therefore not visible). We typically collected highly redundant data to help compensate for this. We also used to correct for absorption by assigning Bragg indices to the crystal and making precise measurements of crystal dimensions.
Scaling programs are now more extensive, and include options to calculate a pseudo-absorption surface. In principle, if you have a beam that is ALWAYS smaller than the crystal, then the same crystal volume is illuminated by the xray beam, and will minimize scaling errors. Bernie Santarsiero On Fri, November 23, 2007 4:34 pm, Jim Pflugrath wrote: > It probably goes back to the days of using a single-counter diffractometer > where one didn't have multiple Bragg reflections on an image or film pack. > That is, each reflection was collected by itself. Even in a small > molecule > crystal data collection nowadays, it would not hurt to have the crystal > completely bathed in the beam. > > Also in the old days (let's say pre-cryo), there was plenty of radiation > damage going on even with a sealed-tube source. We always corrected for > radiation damage by extrapolating back to zero dose in those days. > > Jim > > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Robert > Sweet > Sent: Friday, November 23, 2007 4:08 PM > To: [email protected] > Subject: [ccp4bb] To bathe or not to bathe. > > Jorge, > > You said, > >> I remember one former good (small molecule ?) crystallography book >> with words a kind of this "the crystals should be completely bathed by >> the x-ray beam during the whole data collection" ... > > The original motive for bathing the whole crystal was to assure that the > relative intensity of the data on each successive film pack was very > nearly constant. This was possible (one might say "necessary") in the old > days because the laboratory sources were very stable and the intensity was > low enough that there wasn't a lot of x-ray damage to the crystals. > There were a couple of other good reasons to pay attention to details like > this. One was that methods for scaling images together were not quite as > good as now, and another was that film data were relatively very much less > accurate than what is achievable now with excellent detectors and brighter > sources. To combat all of that, we tried to do everything possible to > make things better. > > These days scaling algorithms are good, the detectors are excellent, and > very often it pays to employ a beam smaller than the x-tal. This, the > non-uniformity of many synchrotron beams, and the systematic damage > to crystals that we observe now with synchrotron sources cause serious > systematic errors. We're forced to depend on good scaling and good > detectors to get accurate measurements. Making the measurements in many > different crystal orientations (redundancy) helps to smooth out these > systematic errors. > > Nonetheless, it will always pay you to watch for EACH of these sources of > error and to minimize them as best you can. > > Bob > > ========================================================================= > Robert M. Sweet E-Dress: [EMAIL PROTECTED] > Group Leader, PXRR: Macromolecular ^ (that's L > Crystallography Research Resource at NSLS not 1) > http://px.nsls.bnl.gov/ > Biology Dept > Brookhaven Nat'l Lab. Phones: > Upton, NY 11973 631 344 3401 (Office) > U.S.A. 631 344 2741 (Facsimile) > ========================================================================= >
