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
> [log in to unmask]
> 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
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