Recently, I had problems getting imosflm to find spots on a low
resolution data set. I found that setting a good beam X and Y value has
a huge impact on mosflm's ability to find spots. Thus, I would manually
set the beam positions right after I added the images and then I would
proceed on to the indexing step. It made a big difference.
Steve
On 9/29/2015 2:39 PM, Edward A. Berry wrote:
> I'm trying to index some weak data with mosflm, mainly just to get
> cell parameters.
> The automatic procedure fails, so I'm trying to modify things
> manually, and having trouble.
>
> I run imosflm (7.2.1 on Fedora 14 ( is that a problem?))
> File menu: load images, select the first image, OK, they all 10 get
> listed in the window
> (the first image has wrong phi angles in header, I can't find how to
> enter phi angles manually or exclude it so rename and start again
> without it)
> click index in the left toolbar. first and last are selected for spot
> picking but autoindexing fails.
> Looking at spots (picked) many don't correspond to visible spots and
> the strongest spots are not picked.
> But quite a few spots are correctly picked, so it is interpreting the
> image (not a byte-swap problem)
>
> I see how to adjust the resolution (in the graphics window) and
> threshold etc in the main window.
> Change these and click the find spots icon in the appropriate image
> (one of the two already selected)
> and the number of spots changes in the expected direction (at least
> for threshold and spot separation)
> But many spots are not picked and I don't know why. There used to be a
> list of which spots were rejected for what reason. Is that still
> available?
>
> So I want to add more images besides the two initial frames. I click
> the 3-images icon in main window and all frames are displayed, with
> check boxes. But they cannot be checked! OK, because spots have not
> been picked for those images. But when I click the find-spots icons in
> those lines, nothing happens! All the frames can be read, because I
> can step through them in the image window.
>
> I'm sure I'm missing some pretty obvious things, but I need help to go
> on.
>
> The images are from oxford xcalibur, exported with dc imgtomar img 50 1
> in mosfilm I would give "detector oxford" But I assume that gets
> detected automagically now.
> For example does mosflm know the phi axis is vertical as the image is
> displayed in the image window?
> But first I need to get spot picking working.
>
>
> Ed
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