Dear Harry, Do you mean that it cannot be done in command line to make picture with prediction boxes? I wrote input file for ipmosflm, by which I had only to click "Predict" to see the predictions on GUI. (I wrote matrix, symmetry and mosaic spread information in the input file!)
Or, how can I get the predictions on the images in command line? Thank you very much, K. Yamashita 2010/12/9 Harry Powell <ha...@mrc-lmb.cam.ac.uk>: > 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 <ha...@mrc-lmb.cam.ac.uk>: >>> 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 >
