Hi Keitaro You should get the predictions on the images using Mosflm if you supply a matrix & spacegroup. Running the "create_image" part after indexing in iMosflm means that the matrix, symmetry and mosaic spread are all available, so it can be easier doing it this way.
There's a very old script under our "FAQ" page for producing a series of images - see http://www.mrc-lmb.cam.ac.uk/harry/mosflm/FAQ.html#movie On 8 Dec 2010, at 14:54, Keitaro Yamashita wrote: > Dear Boaz and Harry, > > Thank you very much for your suggestions. > > As pointed out by Harry, I think it is difficult to automatically make > a picture of spots labeled with their indexes.. > > But I have never known that iMosflm could accept the commands of ipmosflm. > I'm glad to hear that and it worked very fine. > > But when I did the same thing in ipmosflm input file, I got the > picture *without* prediction boxes (only copy of diffraction image). > Of course I input MATRIX file. > > This is the end of output of ipmosflm: > > NeoCtrl => Image will be written to file image.ppm > invert = 0, theta = 0, wide = 3072 > NeoCtrl > =>******************************************************************************** > At the beginning of CONTROL, the arguments have these values: > FIRSTTIME: F IFIRSTPACK: 1 NEWGENF: T GENOPEN: F RPTFIRST: F > MODE: 0 > CELLSTR: > ******************************************************************************** > MOSFLM => > > *** WARNING ** NO "RUN" CARD GIVEN > > > > *********** END OF PROCESSING ***************** > > > I'm using Mosflm 7.0.6. > Since I'd like to automatically make pictures of several frames with > prediction boxes, so I'm trying to do that in ipmosflm. > > Thank you for advice in advance, > > K. Yamashita > > 2010/12/8 Harry Powell <[email protected]>: >> Hi Keitaro >> >> Mosflm has been able to output jpegs with predictions for many years - it >> can also output ppm files (which are not compressed in a lossy way, so >> probably better for zooming in or converting to other formats). However, >> you'd need to add the indices to the prediction boxes manually - I don't >> know a really robust way to automate putting them in in sensible places with >> sensible font sizes etc. for all possible cells. >> >> iMosflm (i.e. the new GUI) itself doesn't have the widgets to do this, but >> if you run an iMosflm job and get at least as far as having indexed and >> estimated (or entered) a mosaicity do the following; >> >> * go to the "History" task >> * click on "Log" (to bring up the light green on green log display) >> * left mouse click in the display >> * <Ctrl>-k to bring up the command entry line >> * enter the following commands >> >> image <image number of the image you want to plot> >> xgui on >> go >> create_image type ppm prediction on binary true filename image.ppm >> (creates a ppm) >> or >> create_image prediction on binary true filename image.jpg (creates a >> jpeg, default) >> then >> return (redirects input back to the normal Mosflm commands) >> >> It's also possible to do this from the normal Mosflm command line or put it >> in a batch file - I often do this to prepare a set of images for movies. >> >> On 8 Dec 2010, at 05:31, Keitaro Yamashita wrote: >> >>> Dear all, >>> >>> I would like to make a picture of diffraction photograph with (hkl) indexes. >>> >>> I found it in Fig. 1 in the paper: Acta Cryst. (2009). D65, 553-559 >>> http://dx.doi.org/10.1107/S0907444909010725 >>> Direct link to the figure: >>> http://journals.iucr.org/d/issues/2009/06/00/dz5158/dz5158fig1.html >>> >>> Can LABELIT, Mosflm or other program make image file (jpg or >>> something) such like that? >>> >>> Thank you very much in advance, >>> >>> K. Yamashita >> >> Harry >> -- >> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills >> Road, Cambridge, CB2 0QH >> Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
