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Thanks everyone, it worked. Sorry for not seeing the obvious On Tue, Sep 29, 2015 at 5:04 PM, Harry Powell <[log in to unmask]> wrote: > Hi Ed > > (*) You can edit the phi angles in the “Images” pane - left-click twice > (i.e. click-pause-click, *not* double-click) on the values you want to > change - the field changes colour and you can enter the values you want. > They will be propagated through all subsequent images in the sector. > > This is documented in the online tutorial (immediately before Section 4 - > Image Display. > > (*) I’d need to see the images to work out why the spot finding is not > working as expected - can you send me a couple off-line? > > (*) If you go to the “History” pane, then select the “Log” tab at the > bottom, a scrollable light-green on dark-green display is visible, and you > can search through this for the reasons why the spots have been rejected. > > (*) If you use the “three images” icon, you select the images (and find > spots on them) by double-clicking the circular icon next to the image - BUT > it’s much more convenient to type the image number(s) in the entry box with > the automatically chosen images. > > (*) You shouldn’t need to convert the Excalibur images to Mar format - > unless Oxford (Agilent, Rigaku…) have changed the format they write their > native images in. We used the Mar converted format for about a month or so > when the detectors were first marketed (in 2003 IIFRC), but Mathias Meyer > spent a couple of days with me then to make sure we could read the native > images properly. > > (*) The image display can be a little confusing - it uses the internal > Mosflm frame of reference, which may not be what you see when looking at > the physical machine - but that shouldn’t be a problem, because we take > that into account when doing the calculations. > > HTH > > Harry > -- > Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick > Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH > Chairman of International Union of Crystallography Commission on > Crystallographic Computing > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing) > > > On 29 Sep 2015, at 21:39, Edward A. Berry <[log in to unmask]> 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 >