| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | Advert | | ||||||||||||||||||||||
XDisplayF (xdisp) |
|||||||||||||||||||||||
- Protein crystallographyMain steps:- Protein purification- Crystallisation Special:- Programs for crystallography- ADSC-software - HKL package - HKL2000 package - XDisplayF - Supported formats - HKL2MAP - X-ray detectors Basic tutorials:- Chemistry- Protein - Peptide - Amino Acids Xtal community:- CCP4BB |
Please note, that XDisplayF is x-window program and it is necessary to have X-Window support. Because xdisp use the x-window interface it is possible to use remote computer as a host computer. Starting XdisplayF (xdisp)XDISP in an alias for running XDisplayF program. Simplest way to run this XDisplayF it is necessary to type next command string:xdisp FORMAT Image_Name, where FORMAT is the format of the X-ray data image. All supported by xdisp formats are listed here: Formats supported by xdisp. It is possible to have a list of all supported programs by typing in the command litne xdisp. Image_Name - Name of the X-ray data image with path to this image. Another options to run xdispIt is possible to launch the program with the Image_Name specified with variable number, according to standard numbering scheme.xdisp FORMAT Image_Name###.ext number - in this case the sign ### will be substituted by number. xdisp FORMAT Image_Name###.ext number Image_Name###.x - in this case the sign ### will be substituted by number. - Image_Name###.x - List of integrated reflections from Denzo output. In the ImageWindow you can click "Update Pred" and prediction will appear on the screen. Communication between xdisp and DenzoDenzo and xdisp communicate between each other through the hklprediction ans .test files, that is why it is necessary to use the same directory to run Denzo and xdisp.XDisplayF (xdisp) window descriptionAfter proper running xdisp the window with image will appear. The name of the image will be on the top of the xdisp window. Here you can read description of all buttons and outputs in the xdisp window. Despite this full description it is much more useful to became more familiar is to play by yourself with this xdisp window. In case if everything goes wrong - just kill this window by clicking close button and rerun the XDisplayF program again.![]() This is a top part of the XDisplayF program window. Please note, that the button alignment on this window is depends from the image displayed. At the top part of window, the image name is displayed.
Zoom window of XdisplayF (xdisp)
Other XdisplayF (xdisp) functions 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. 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. The function of this button is completely opposite to the Floor up button. Invert the image display. Operate with gray and color images (see color button). 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.
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. 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. 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. Shows overfilled pixels by RED color. 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..
This function was never used in our research activities. Displays menu with help topics organized as submenu. Not very useful yet. To close help menu - click Help button again. 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. 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 the XDisplayF program. 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.
|
||||||||||||||||||||||
| ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd |