Hi Keitaro perhaps we should discuss this discreetly off-board!
Yes, you can make a picture on the command-line with prediction boxes. I do it frequently. If I take one of our example HypF images (see http://www.ccp4.ac.uk/autostruct/testdata/mosflm/hg_images.tar), then on the command line I can - >> matrix r3.mat >> symm r3 >> image hg_001.mar1600 >> xgui on >> go >> create_image type ppm prediction on binary true filename junk.ppm >> return >> exit where "r3.mat" is a matrix file produced from indexing with Mosflm and contains - >> -0.00443809 -0.00922337 0.02048824 >> -0.01923344 0.01406363 0.00304649 >> -0.00630639 -0.01210521 0.00058584 >> 0.000 0.000 0.000 >> -0.2141751 -0.5582786 0.8015324 >> -0.9281747 0.3719797 0.0110743 >> -0.3043363 -0.7415902 -0.5978489 >> 62.0720 62.0720 62.0720 56.3041 56.3041 56.3041 >> 0.000 0.000 0.000 and I get an image (converted to a jpg to reduce bandwidth hogging) - http://www.mrc-lmb.cam.ac.uk/harry/junk.jpg On 8 Dec 2010, at 16:03, Keitaro Yamashita wrote: > 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 <[email protected]>: >> 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 >> Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
