Before any further attempts you must check that the crystals have the same unit cell volume. I usually do this using matthewscoeff from the GUI ( By the way why isn't the volume automatically written into the mtz header asap!!!)
If the cell volumes differ by as much as 5% no reindexing or any other trick will be able to get those data sets to scale together. However if the cell volumes are similar then you may well be able to get a different indexing scheme which will match them. pointless will try to do this, or if all else fails you can run the old MR program almn, with two data sets as input and it will suggest how they mitt be related.. Eleanor PS Phil is too despondent about output from scale pack into aimless. (use the scale pack option NOMERGE to get an unmerged but scaled set of intensities.) SCALEPACK will already have done the internal scaling so you only need aimless to get scales between the different passes. Eleanor On 2 Aug 2012, at 15:53, Uma Ratu wrote: > Hi, Micheal: > > Thank you for your comments. I am getting to know where is the problem. Sorry > that I did not give the information of my datasets in details. > > Here are the answears of the some of the concerns: > > > 1) putative space group? > P2 or P21. > > > 2) observed resolution > 50 - 1.5 A > > > 3) how big was the crystal and what was its shape? Was the crystal split? > Crystals is abot 100 um x 20 um x 20 um. Thesy are thin rods. The crystal is > not split. > > > 4) were the data sets taken at different points on the crystal? Is > > radiation damage a factor? > > The data sets were taken at different points on the crystal. > > Radiation damage is not a facotr. > > > 5) did you just rotate around phi (or omega) to collect the different data > > sets or did you change the other angular settings? > > Collections were taken at one direction along the long side of the crystal, > at diffrent spots. > > > 6) are all your data sets indexed in exactly the same way > > Yes, each can be index and intergrate individually without any probelm using > HKL. But I can not combine them togehter using just one standard. I notice > that the cell deminsions are diffrent from these sets. As you and other > suggested, non-uniformity in a large crystal may be the cause. I will try to > use other program as suggested by many of you. > > Thank you very much for all your inputs > > Uma > > > > On Thu, Aug 2, 2012 at 9:04 AM, R. M. Garavito <[email protected]> wrote: > Uma, > > Before this discussion goes much further, you need to provide more details: > > 1) putative space group? > > 2) observed resolution and diffraction anisotropy? > > 3) how big was the crystal and what was its shape? Was the crystal split? > > 4) were the data sets taken at different points on the crystal? Is radiation > damage a factor? > > 5) did you just rotate around phi (or omega) to collect the different data > sets or did you change the other angular settings? > > 6) are all your data sets indexed in exactly the same way (a tricky and > non-obvious factor for a novice to appreciate). Using pointless on unmerged > data sets helps with this. > > You have a number of unknowns here, and your problem in merging the data sets > may be due to radiation damage, non-uniformity in a large crystal, index > refinement problems due to diffraction anisotropy, etc. We routinely merge > different data sets from a single crystal, which has been translated and > rotated about one axis only. We try to index and process the data sets using > a common setting matrix (which is easy with XDS). However, sometimes it just > does work, but merging pairs of data sets often allowed us to discard the > worst offender(s). > > Good luck, > > Michael > > **************************************************************** > R. Michael Garavito, Ph.D. > Professor of Biochemistry & Molecular Biology > 603 Wilson Rd., Rm. 513 > Michigan State University > East Lansing, MI 48824-1319 > Office: (517) 355-9724 Lab: (517) 353-9125 > FAX: (517) 353-9334 Email: [email protected] > **************************************************************** > > > > > On Aug 1, 2012, at 4:37 PM, Uma Ratu wrote: > >> I notice one thing with my data sets. >> >> The unit cells is slightly different from each other. For example, one has >> a/b/c @ 79/126/83. The other has a/b/c @ 84/127/90. Although they are >> collected from the same crystal. >> >> Is this the reason that I can't index both with same parameter in HKL? And >> subsequently, can't integrate and scala together. If so, is there a way that >> I can fix it? >> >> Thank you for your advice >> >> Uma >> On Wed, Aug 1, 2012 at 8:50 AM, Uma Ratu <[email protected]> wrote: >> Dear All: >> >> I collected 5 data sets from one crystal and would like to process them >> together. >> >> Here is how I did: >> >> In HKL2000, load the all data sets. "Index" each set. When I try >> "Intergrate", the program automatically go through the whole data sets >> there, and do not go through. >> >> I then process data sets by loading one at each time. Index, intergrate and >> scale all go through very smoothly. But when I put them together, the >> program just goes crazy. >> >> Thank you for advice >> >> Uma >> > >
