XDisplayF (xdisp)

Main steps:

Special:

Basic tutorials:

Xtal community:

Starting XdisplayF (xdisp)

Another options to run xdisp

Communication between xdisp and Denzo

XDisplayF (xdisp) window description

• Prof fit R Allow to turn on/off the profile fitting radius. This function is working when the prediction is already done. The only spots stronger than WEAK LEVEL, according to Denzo are shown. For definition of PROFILE FITTING RADIUS refer to the Denzo manual. These two X-ray diffraction pattern with prediction shows the xdisp window with and without Prof fit R:
  

  Lysozyme X-ray diffraction pattern with Prof fit R OFF	Lysozyme X-ray diffraction pattern with Prof fit R ON

Zoom window of XdisplayF (xdisp)

• Zoom wind This button is responsible for launching of ZOOM WINDOW. The size of the ZOOM WINDOW can be adjusted from inside this window. Position of the centre of the ZOOM WINDOW can be selected by mouse middle-button click either in main window, ether in ZOOM WINDOW.
  
  

  X-ray diffraction pattern with Zoom window switched ON. It is possible to see the square place, represented the zooming area.	Related Zoom window.	The papers-suitable representation of the X-ray diffraction pattern with Zoom window.

  
  Within Zoom window all three mouse buttons are active: Middle mouse button select new centre for the Zoom window; Right mouse button displays the cross-sections through the position of the mouse pointer, to see the 2D profile of the Zoom window; Left mouse button display all information about clicked point and, if this point is related with reflection - displays the h, k, l parameters.
  

  The 2D profiles for the xdisp Zoom window, which allow to see real signal/background ratio.	Information about "empty space".	Information about predicted reflection.

  
  Zoom window contains the following operational buttons:
  
  
  • Zoom in Increase the magnification of the Zoom Window by factor of 2. when the magnification factor exceeds 32, the digital pixel intensities will be displayed on the top of the pixel pattern.
    
    

    Zoom Window with high magnification. Digital pixel intensities are shown.

    
    
  • Zoom out Performs function opposite to the Zoom in button: Decrease the magnification of Zoom window.
  • Int. box Perform the different mode of showing of integration box. Each clicking of this button changes the mode of spot showing. The size of integration box and integration circles are defined by denzo parameters BOX and SPOT. Check denzo manual about the definition of these parameters.
    

    The default integration box shows circles centred on predicted places. The size of these circles is 6 pixels. Color scheme is standard: green - fully recorded reflection, yellow - partially recorded reflection, red - rejected reflection.	Next window: In addition to the colored circles with predicted reflection positions the Integration box, Integration circle and Integration background circle are shown with real sizes.	Next window: The Integration box is removed. Integration circle - colored white and Integration background circle colored red. Circles with predicted positions are also shown.

    
    
  • Diff Vec
  • Zoom close Safely close Zoom window. Other ways to kill Zoom window can results in closing all xdisp windows.
  • Help This is very informative interactive help system which is still not implicated in full yet. Please be patient for another few years.

    Help for Zoom window - bad alignment, not full.	Example of Help window for Zoom in command.

    
    

Other XdisplayF (xdisp) functions

Write/Print Write to the HDD file with current image in the .XWD format. XWD - X Window Dump. For our studies we newer use this option, but instead we've use Window Grab function implemented into XV viewer, or we've use Alt-Ctrl-PrintScreen to grab the xdisp window from the windows operational system.

A/D test

Floor Up Lift up the lower level for the intensities display range. The image pixels with intensities below the current floor will displayed at lowest color or darkness level. This effectively reduces the displayed range, but increase the contrast of the output image. The left, middle, right click of the mouse cause small, medium and large changes, respectively.

Floor Down The function of this button is completely opposite to the Floor up button.

reverse Invert the image display. Operate with gray and color images (see color button).

color Change image presentation between black & white and color mode. The selection of the best mode for image presentations depends from personal preferences of scientist, but for the publications the best mode of presentation is the dark reflection on the white background.

Example of XDisplayF window with default presentation	Example of XDisplayF window reverse mode	Example of XDisplayF window color presentation	Example of XDisplayF window with reverse and color presentation

Remove pred and Update pred Switch OFF and ON X-ray diffraction prediction. The prediction is automatically updated from the denzo output. Predicted reflections are shown by circles with different colors: green - fully recorded reflections, yellow - partially recorded reflections, red - rejected reflections.

Full scale Change scaling of the image from optimal to full to show the relation between the actual data collection and detector abilities. This function is not always worked correctly.

Go Run the subsequent image changes. The direction for image numbers to change is defined by the status of the Frame button. - for the increase image numbers, and - for decrease image numbers. This function work properly with images, numbered accordingly standard file name mask: filename###.ext , where ### - number of the image.

Show Overfl Shows overfilled pixels by RED color.

Peak Sear Search peaks on the displayed image. Results are stored in the file peaks.file. After running of this routine, the selected peaks are circled by bold red circles and on the right side of the image the control menu will appear. During the time of program calculation, the information about program status will be displayed with the Peak searching ... button: and the picture of very clever man (see the end of this manual) Please note, that these peaks are starting peaks for the denzo indexing and this set should be selected carefully..

Window with found peaks. Selected peaks are circled red. The right hand side menu is described below.

• Ok Finish the Peak search routine and create file peaks.file with selected peaks. The current number of peaks is displayed just above the Ok button. Example: 944 spots found:
• More peaks Reduce the accepted level (intensity to background) of peaks which results in increasing number of peaks found. When the accepted level is near to the background, XDisplayF can accidentally crash, and it is necessary o run it again.
• Fewer peaks Opposite to the More peaks routine.
• Size peak up Increase the size of searched spots. This is necessary when the crystal diffraction pattern appears with unusually large spots.
• Size peak down Reduce the size of searched spots. This is necessary when the crystal diffraction pattern appears with unusually small spots and the distance between these spots is extremely small.
• Pick (Add) Allow to add manually peaks, by clicking in the main window or in the zoom window in close vicinity from the spots, not selected by automated routine.
• Pick (Remove) Allow to remove manually peaks, by clicking in the main window or in the zoom window in close vicinity from already selected spots. This is useful to eliminate problems related with data collected from multi-crystals, or for data collected from crystals with ice-rings.

Edit P.S. This function was never used in our research activities.

Help Displays menu with help topics organized as submenu. Not very useful yet. To close help menu - click Help button again.

dim Function is opposite to bright. Increases the intensities range to display with reducing intensities for strong spots representation. A lot of clicks to this button will result in clean of whole image.

bright Function is opposite to dim. Decreases the intensities range to display with improving of weak spots representation. A lot of clicks to this button will result in darkening of whole image.

close Close the XDisplayF program.

Frame and - controls the direction of automatic number changes activated by Go button. Left mouse click set this button to Frame down position, right mouse click set this button to Frame up position and middle mouse button click cause of one frame change, according to selected direction. Work properly only with standard image names filename###.ext, where ### - image number.