Re: [ccp4bb] superposing (hkl) indexes on diffraction image
Dear all this is *really* embarrassing for me. It's just been pointed out to me (and also demonstrated...) that this script won't produce the predictions as I suggested it would. In order to make an image with the predictions on, you need an extra line in the script - matrix r3.mat symm r3 image hg_001.mar1600 xgui on go predict_spots create_image type ppm prediction on binary true filename junk.ppm return exit Thanks to the anonymous user (still wearing shorts, even in February...) who pointed this out! On 8 Dec 2010, at 16:16, Harry Powell wrote: 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 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
Re: [ccp4bb] superposing (hkl) indexes on diffraction image
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
Re: [ccp4bb] superposing (hkl) indexes on diffraction image
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
Re: [ccp4bb] superposing (hkl) indexes on diffraction image
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
Re: [ccp4bb] superposing (hkl) indexes on diffraction image
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
Re: [ccp4bb] superposing (hkl) indexes on diffraction image
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 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:
Re: [ccp4bb] superposing (hkl) indexes on diffraction image
Keitaro, The Python script we used to make Fig. 1 is contained within the Labelit source code distributed with Phenix, in the file labelit/publications/sublattice/sublattice_Fig1.py The PDF-generating code was never made into a finished product; at present the most important missing element is that the hkl indices are reported in the primitive setting, not the final setting if your lattice is other than primitive. Given a couple of weeks I can implement this. In the meantime, the existing code can label spots in the primitive setting and produce publication-quality PDF files. Example usage is: labelit.index image file name \ sublattice_pdf_file=./Fig1.pdf \ sublattice_pdf_render_all=False \ sublattice_pdf_window_fraction=0.18 \ #Plot edge is 18% of the entire image sublattice_pdf_window_offset_x=0.532 \ #Plot center, as a fraction of the entire image sublattice_pdf_window_offset_y=0.5 \ sublattice_pdf_box_linewidth=0.8 \ sublattice_pdf_enable_legend=True \ sublattice_pdf_enable_legend_font_size=9 \ sublattice_pdf_enable_legend_ink_color=black \ sublattice_pdf_enable_legend_vertical_offset=9.5 \ image_brightness=0.7 Regards, Nick Sauter On Tue, Dec 7, 2010 at 9:31 PM, Keitaro Yamashita yamash...@castor.sci.hokudai.ac.jp 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
[ccp4bb] superposing (hkl) indexes on diffraction image
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
