The default mode of autoindexing in HKL2000 and denzo is to search for unit cell lengths producing spots that can be resolved at the data collection distance and with the specified spot size (it can be changed in HKL2000 interface). If the unit cell of your crystal is significantly longer, the program will not find it. Considering that your spots are not well resolved, it is a quite likely possibility. Your diffraction extends to less than 3A, so pushing detector back will not cause any loss of the measured diffraction. The logic of limiting the unit cell length in autoindexing is that indexing will fail when data cannot be integrated due to spot overlap resulting from a long unit cell. Another possibility is that your crystal has some type of severe packing disorder along the long axis. In such a case, there is probably no point in collecting a dataset.
Autoindexing in HKL2000 is a multi-step process. Not all the found peaks you have shown in your diffraction image will be used for autoindexing, as they have also to pass the signal-to-noise cutoff in denzo. The ones accepted for autoindexing are shown in a subsequent window in green color. You can also use a resolution limit to eliminate peaks at higher resolution during autoindexing and then extend the resolution during the refinement. Sometimes it helps for very mosaic crystals. Zbyszek Otwinowski > Dear colleagues, > > I am working on one dataset that is hard to process. The data are about 3A of resolution. As we are not able to reproduce the experiment again, I have > to use this one, collected in a dirty way. > The problem starts immediately with finding of spots. I have tried HKL2000, > XDS, D*trek, ipmosflm, imosflm, but none of them gave a good read-out of the > images. All the programs find some spots in wrong positions and the real spots are not covered. Here is an example: > > http://kolda.webz.cz/image-predictions.jpg > > The data were collected in-house, Saturn 944++ CCD, and all the necessary information should be in the header properly. I checked the distance, other > parameters, but the problem is with finding of "correct" or "real spots" on > the image. This should be even header-independent, should not? All the programs fail (or even crash) in this routine. Does anyone have any suggestion, please? > > Btw, we have several structures in the PDB from this experimental setup. This is the first problem I have met. > > Many thanks for any response. > > Petr > > -- > Petr Kolenko > [email protected] > http://kolda.webz.cz > Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
