Development of the software is continuing. This documentation is for Version 1.34, released September 2000. Comments on the programs themselves, and on this documentation, are welcome; send them to Marian Szebenyi.
To process a set of data, type "process" for an initial run. If you already have a parameter file (created by a previous run of the program), you can type "process name", where "name.param" is the name of the parameter file. Process is a script that copies the necessary shell scripts ("command files") from a standard location to the current directory (if they're not already there), starts up processing_gui, and loads the specified parameter file, or a standard prototype if no filename is given. The main interactive window, part of which is shown here, will come up.
Processing_gui stores information in a parameter file, whose name generally (but not necessarily) has a ".param" extension. This file is updated during processing and can be read in on a subsequent run. Area (1) of the main window allows you to specify a parameter file, load parameters from the file, and save parameters to the file. If you specify a non-existent file and click "SAVE", a new file will be created. It is good practice to make a new parameter file for each dataset: start by loading a file from a similar dataset, or the prototype, change parameters as necessary (see below), change the file name, and save it.
A number of "command files" are needed to run the various programs which are part of the system. These are kept in a standard location and copied to the current working directory before use. This is done automatically by the process script, but can also be done manually by clicking the "Get Cmd Files" button (2). You may need to do this if you have edited the command files and want to reset to the standard values, for instance. To edit command files before executing them, click "Edit Cmd File Before Execution". See command files section for much more about command files.
Area (3), and the "Directories:Images" field above it, specifies the image files to be processed. Files are sought for in the "Images" directory, and filenames are of the form "prefix_run_sequence.suffix", where "prefix" is given by the "Image Prefix" field, "run" by the "Run No." field, suffix by the "Filename suffix" field in the "Detector Parameters" window (see below), and "sequence" runs from "Start Image No." to "End Image No.". Alternatively, the "Run No." field may be left blank and filenames are of the form "prefix_sequence.suffix". For indexing, and initial refinement, "sequence" generally covers only a few frames; change to the complete range before integration.
Area (4) contains a few basic parameters for this dataset. Other parameters are shown, and can be changed, in the windows which you can pop up using the buttons at the top right (5). In particular, be sure to set the correct detector type in the "Machine Parameters" window. To change a parameter, type the new value in the appropriate text field. To save updated parameters to the current parameter file, click "SAVE". To save them to a new parameter file, enter a new name in "Parameter File" and click "SAVE".
To stop a process which has been started from the GUI, click "STOP". To exit from the GUI itself, click "CLOSE" (6).
Follow the flow chart across the middle of the GUI: indexing, refinement, integration, scaling, final output.
When setting the detector type, be sure to also set the direction of rotation and orientation of the spindle axis, in the "Machine Parameters" window. These depend on the particular camera on which the detector is mounted. At CHESS, for example, the spindle orientation is always horizontal, but the rotation direction is clockwise at the F-1 and F-2 stations and anticlockwise at A-1.
The indexing process includes visual inspection of one or more diffraction patterns, location of diffraction spots, and determination of the unit cell parameters and orientation of the crystal that produced the image(s). Two means are available for this operation; they are described below under the headings of Index:DPS and Index:MOSFLM. DPS indexing usually works well and requires only one image. Mosflm indexing gives the options of DPS or REFIX indexing. DPS indexing via differs from direct DPS indexing in the peak search routine used, and in the pre-refinement which mosflm does immediately after indexing; REFIX-style indexing is more touchy and often requires more than one image to succeed.
In either case, activation of an indexing button first checks for the existence of the image files specified by the "Images" (directory), "Image Prefix", "Run No.", "Start Image No.", "End Image No.", and "Filename suffix" (in the "Detector Parameters" window) fields. Filenames are of the form "prefix_run_sequence.suffix" (run number given) or "prefix_sequence.suffix" (run number field blank), where "sequence" runs from "Start Image No." to "End Image No.". If any of the files do not exist in the image directory, an error message will appear in the message window:
Index: DPS |
DPS indexing works on one or more images. By default, it will use the image specified in the "Start Image No." field, and the starting phi and delta phi values from the Machine Parameters window. If this is a good image and the program is using the correct distance, wavelength, and direct beam position, a good solution can generally be obtained. If not, you can select a different image, or use multiple images. At the top of the Autoindexing window is a field labeled "Frame[:phi]'s to Use". In this field specify the images you wish to use, separated by spaces. Each image can be given as either a single number or as two numbers separated by a colon(:). If two numbers are given, the first is the image number and the second is the starting phi value for that image. If one number is given, the starting phi is calculated from the image number, assuming that all images have the same delta phi, there are no discontinuities in the sequence of images, and the image specified in "Start Image Number" has the starting phi given in the Machine Parameters window.
If you know the unit cell of your crystal, you may enter it in the "target cell" field and turn on "Use target cell". The indexing routine will not strictly enforce the given cell, but will favor solutions near to that cell. If no good solutions are close to the target cell, "Use target cell" has no effect.
To proceed with indexing, follow the sequence of buttons below the frame selection field.
"Find Peaks" starts up the adxv display program. You should see a control panel, a window titled "Adxv Predictions", and a display of the first image to be used for indexing. (If the image window is blank, try clicking "Auto" in the "Scale" section of the control panel. You may also need to do this if the image window has been obscured and then uncovered.) Be sure the cross indicating direct beam position is on the direct beam spot. To check it, zoom in on the area around the direct beam by clicking on the beam spot with the right mouse button. If the cross is not centered on the spot, use the "Settings" item of the "Edit" menu to bring up a window for adjusting the cross's position. If it is way off, type in approximate mm coordinates of the direct beam spot. Use the arrows for small adjustments in the cross's position. Click "Fix Settings" to use the new position on any subsequent images.
If you do not know the lattice parameters of your crystal, you can estimate some of them at this time: Select a line of spots whose lattice spacing you wish to check. Zoom in on the area around the line. You may need to expand the "Magnify" window (using the window manager "handles" at the corners of its frame). Place the mouse at one end of the line, hold down the left button, and drag it along the line. A new window will appear, containing a plot of pixel values along the line, and the corresponding lattice spacing. If you drag the mouse along another line, the plot will be updated to show the new line. Note that you must have the correct distance, direct beam position, pixel size, and wavelength (in the "Settings" window) for the calculated lattice spacings to be correct. Also note that adxv is not aware of the "Two Theta" setting, and lattice spacings will be incorrect for Two Theta substantially different from 0.
In the "Adxv Predictions" window, click on "Find Peaks" to perform the peak search. Found peaks are displayed in blue on the image. If there are too many or too few peaks, adjust the parameters (maximum number of spots, minimum I/sigma(I), minimum spot separation) above "Find Peaks" and click the button again. It is also possibly to manually edit the spot list: click "Add Peaks" or "Remove Peaks" in the "Manual Peak Picking" section, then click on the particular spots you want to add or remove. If you close the "Predictions" window, you can use the "Predictions" item of the "View" menu to bring it up again. Indexing works well with 500-1000 peaks, provided that there are that many good spots on the image; a small unit cell or poorly diffracting crystal may give fewer.
If you are indexing on more than one image, use the "Load" item of the control panel's "File" menu to bring up a file selection box. Load the next image file you want to use by double-clicking on its name. Click "Find Peaks" in the predictions window to store peaks from this image. Repeat for each image that you want to use for indexing. Peaks for each file are stored in a file image_name.peaks, where image_name is the name of the particular image file; this file is kept until explicitly deleted or until overwritten by another peak search on the same image. This means that if you want to reindex with a different selection of files, you need only do a peak search on files which have not been used in any previous indexing.
After finding peaks, you can exit from adxv, using the "Exit" item in the "File" menu of the "Adxv Control" window. Confirm that you really want to exit. If you don't exit now, adxv will be terminated automatically when you start actual indexing.
Set the "Maximum Cell Edge" field to be comfortably larger than the longest unit cell edge you expect to have (e.g. for a longest cell edge of 250 Angstroms, enter 300). If you don't know the unit cell parameters, get an estimate using adxv (see above), or just use 300. Adjust the resolution limits for indexing if necessary: usually it is appropriate to have a wide range and use all the picked peaks, but you may have to limit resolution if you can't come up with peak-picking parameters that find enough real peaks without picking up too many noise peaks, or to avoid using spurious peaks from ice rings. Then click "Autoindex". Possible solutions in different symmetries will be listed:
Primitive Cubic : 6.48 : 55.98 62.22 129.92 90.25 90.84 89.79 82.71 82.71 82.71 90.00 90.00 90.00 I Centered Cubic : 11.82 : 140.71 83.85 143.80 71.92 34.13 75.25 122.79 122.79 122.79 90.00 90.00 90.00 F Centered Cubic : 14.58 : 154.92 153.70 154.00 132.29 65.49 137.46 154.21 154.21 154.21 90.00 90.00 90.00 Primitive Rhombohedral : 6.32 : 62.22 55.98 130.04 89.16 89.72 89.90 82.75 82.75 82.75 89.59 89.59 89.59 R Centered Hexagonal : 6.32 : 83.54 140.71 155.55 128.98 87.06 105.04 112.12 112.12 155.55 90.00 90.00 120.00 Prim Trigonal/Hexagonal: 5.70 : 55.98 62.22 129.92 89.75 90.84 90.21 59.10 59.10 129.92 90.00 90.00 120.00 Primitive Tetragonal : 1.27 : 55.98 62.22 129.92 90.25 90.84 89.79 59.10 59.10 129.92 90.00 90.00 90.00 I Centered Tetragonal : 4.07 : 55.98 62.22 271.98 76.98 78.89 89.79 59.10 59.10 271.98 90.00 90.00 90.00 |
Primitive Orthorhombic : 0.27 : 55.98 62.22 129.92 90.25 90.84 89.79 55.98 62.22 129.92 90.00 90.00 90.00 |
C Centered Orthorhombic: 1.23 : 83.85 83.54 129.92 89.62 90.75 83.96 83.85 83.54 129.92 90.00 90.00 90.00 I Centered Orthorhombic: 4.43 : 55.98 62.22 271.98 103.02 101.11 89.79 55.98 62.22 271.98 90.00 90.00 90.00 F Centered Orthorhombic: 3.14 : 83.85 83.54 271.98 92.22 107.21 83.96 83.85 83.54 271.98 90.00 90.00 90.00 Primitive Monoclinic : 0.12 : 55.98 62.22 129.92 90.25 90.84 89.79 55.98 62.22 129.92 90.00 90.84 90.00 C Centered Monoclinic : 1.11 : 83.85 83.54 129.92 90.38 90.75 96.04 83.85 83.54 129.92 90.00 90.75 90.00 Primitive Triclinic : 0.00 : 55.98 62.22 129.92 89.75 89.16 89.79 55.98 62.22 129.92 89.75 89.16 89.79 |
Expect a penalty under 0.5 for the correct symmetry, for a good image and correct machine parameters. If the image is weak, or there is an error in distance or direct beam position, a penalty in the range of 0.5 to 1.0 may be obtained for the correct symmetry (see below for a more complete discussion of this point). In this example, primitive orthorhombic is the most likely symmetry.
The entry for the symmetry currently specified in the parameter file will be highlighted. To change symmetry, click on the appropriate entry. This will update the symmetry entries in the parameter file and the Cell Parameters window. To save the results from autoindexing (whether or not you have changed symmetries), click "Save Result" (in the Autoindexing window). To check how well predictions using these results match the actual pattern, click the "Display Result" button.
Display Result |
Clicking the button will start up mosflm in an xterm window titled "Xmosflm". Type "@display.inp" in the Xmosflm window. When the image appears, click "Predict" to see predicted spot positions. Fully recorded reflections appear blue, partials are yellow, spots very near the spindle axis are green, and overlapping spots are red. Note that the image in this display is rotated 90 degrees from the view seen with adxv, so that the spindle axis is vertical.
To check the precise alignment of predictions with spots, you can zoom in on an area by clicking the "Zoom" button; define the area to be magnified by putting the mouse on its top left corner, holding down the left button, and dragging to its lower right corner. To unzoom, click once on Zoom to change it to Full, and then again (on the button now labeled Full) to execute.
You can get an idea of the mosaicity of your crystal now by looking at the real and predicted spots along a lattice row. If there are extra predicted spots at the end of the row, the mosaicity being used is too high; if there are real spots which are not being predicted, the mosaicity used is too low. To estimate the correct value, change the "Mosaicity" field in the "Processing params" list and click "Predict" again. Repeat until predicted and real spots correspond as well as possible. For integration, use a mosaicity value slightly above this.
The effect on the predictions of changing other parameters than mosaicity may also be examined. For a parameter in the "Processing params" list, click on the old value, type in a new value, and hit C/R to store it. For a parameter not on the list, click "Keyword input" to bring up a dialog window, type the parameter name and value (e.g. "separation 0.4 0.4"), hit C/R, then type "go" to close the window and return control to the mosflm interface. Click "Predict" to see the prediction using the new parameters. Note that many mosflm parameters are not transmitted to processing_gui when you exit mosflm - be sure to update parameters in the "Machine Parameters" and "Integration Parameters" windows to match any modifications that you make in mosflm parameters and want to keep.
To examine predictions for another image, click "Read image". In the dialog window which appears, request another image (e.g. 10). Accept the default phi values, unless there was a discontinuity in data collection and they are not right; click "Predict". Repeat for other images if desired.
After checking predictions, click "EXIT" and answer questions (yes, you do want to save information in a mosflm save file, and yes, you do want to exit). If you want to determine a strategy for data collection, do it now (see "Strategy" section for details). Then type "end" in the Xmosflm window. Finally, use the "CLOSE" button to remove the autoindexing window.
Try using different image(s). Some images, particularly from a mosaic crystal, do not provide enough information for accurate determination of all cell and orientation parameters. Use of multiple images will alleviate this problem; they should be separated by at least 10 degrees or so in phi - be sure to associate the correct phi values with each frame.
Other things that may help are to to pick more or fewer peaks on each image, to change the resolution limits for indexing, or to vary the "Maximum Cell Edge" value. In particular, for large cell dimensions it can help to increase the maximum cell edge, to as much as twice the actual value.
Index: MOSFLM |
Mosflm 6.01 has two indexing options; the "new" indexing is DPS indexing, and you will get essentially the same result using it as you do using "Index: DPS", the only differences being in the peak search routine and in the "pre-refinement" of a few parameters that mosflm does after indexing. The "old", or "REFIX", or "Kabsch" indexing is discussed here.
This indexing uses one or more images. It is less reliable than DPS indexing for a single frame but will generally succeed if you can give it enough images which are separated by at least several degrees in spindle angle. To use, click on "Index:MOSFLM". An xterm titled "Xmosflm" will appear. At the MOSFLM => prompt, type "@index.inp".
A large window will appear with a display of the first image and a number of control areas. Note that the image is rotated 90 degrees from the display in adxv, i.e. the spindle rotation axis is vertical in the mosflm display if it is "Parallel with: Horizontal" in the "Machine Parameters" window.
Image display parameters are controlled by the panel above the image. To change minimum or maximum value, click on the number, type a new value, and hit C/R. To adjust the contrast, use the slider. To change the color scheme, click on the triangle with the right mouse button and select from the menu. The "Mag" menu refers to the magnification in the small image at the top left of the main one, which is a display of the area immediately around the mouse's current position. Note - this area can be enlarged by clicking in it with the middle mouse button. To zoom in on an area, click on Zoom and define the rectangle to be displayed by putting the mouse on its top left corner, holding down the left button, and dragging to its lower right corner. To unzoom, click once on Zoom to change it to Full, and then again (on the button now labeled Full) to execute.
Clicking on a spot in the image displays its coordinates in the Output block to the lower left of the image. The red circle indicates the beamstop position, as specified in the parameter file. The processing parameters down the lefthand side come from the parameter file. They can be changed by clicking on the value to change, typing the new number, and hitting C/R. Buttons in the "Main menu" block control actions.
To get the direct beam location: zoom in on the central region and click on the direct beam spot. The XC,YC coordinates in the "Output" panel are the values you need. Transfer them to the "Beam X" and "Beam Y" fields in the "Processing params" area of the mosflm display, and also to the "X Beam" and "Y Beam" fields in the "Machine Parameters" window of the main GUI. Be sure that the mosflm coordinate system is selected in "Machine Parameters" when doing this.
For REFIX-style indexing, it is suggested that you use two images (if available), preferably well-separated in phi. Starting from the display of the first image, proceed as follows:
Click on "Find spots". An "xdl_io_window" will come up with some information about spot-finding. A narrow red box will appear on the image showing where data for a radial background correction will be taken. If the box overlaps an unusable strip between CCD modules, answer "n" to the question in the xdl_io_window, change the "Y offset" parameter, and click "Find spots" again. If box location is correct, answer "y" to the question.
A summary of spots found on the first image will appear in the window. Hit C/R to dismiss the window and continue. Picked spots show as red crosses on the image display. If the number of spots is too large or small, change "Threshold" and try again.
To index using spots from a single frame, click "Autoindex" now. To use spots from a second frame also, first do this:
Click "Read image". In the window that comes up, request another image (e.g. 10). Accept the default phi values, unless there was a discontinuity in data collection and they are not right. Repeat "Find spots" for this frame. Then click "Autoindex".
In the window that comes up when "Autoindex" is activated, answer "n" to "use new indexing?", answer "y" to "fix detector distance?", accept the default output filename (test_1.mat, e.g.), and confirm that it is OK to proceed. Another window will come up with results of indexing.
List of possible Laue groups, sorted on penalty index. The lower the PENALTY, the better Only solutions with PENALTY less than 200 are listed, a complete list is given in the terminal window No PENALTY LATT a b c alpha beta gamma Possible spacegroups 10 122 oC 84.41 84.42 130.81 89.9 90.2 84.1 C222,C2221 9 122 tP 56.51 62.71 130.81 90.1 90.2 90.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212 8 119 mC 84.41 84.42 130.81 90.1 90.2 95.9 C2 7 119 mC 84.41 84.42 130.81 89.9 90.2 84.1 C2 6 6 oP 56.51 62.71 130.81 90.1 90.2 90.0 P222,P2221,P21212,P212121 5 6 mP 56.51 130.81 62.71 90.1 90.0 90.2 P2,P21 4 5 mP 62.71 56.51 130.81 90.2 90.1 90.0 P2,P21 3 2 mP 56.51 62.71 130.81 90.1 90.2 90.0 P2,P21 2 0 aP 56.51 62.71 130.81 89.9 89.8 90.0 P1 1 0 aP 56.51 62.71 130.81 90.1 90.2 90.0 P1 Select a solution AND a spacegroup from list above (eg 3 p42) or 0 to abandon or T to change min I/sig(I):6 P212121 Running refix again with this symmetry imposed New orientation matrix written to (Keyword NEWMAT):test_1.mat Using 1706 indexed reflections, final sd in spot positions is 0.05mm and in phi 0.24 degrees Refined cell parameters 56.47 62.71 130.74 90.00 90.00 90.00 Do you want to update cell parameters (Y): Do you want to accept this solution (Y) : |
Pick the solution of highest symmetry with a reasonable penalty - generally there will be an obvious break between high-penalty bad solutions and low-penalty good solutions. Type the number of the line with the highest symmetry good solution and a space group name, e.g. "6 P212121". Assuming cell parameters look reasonable, answer "y" to the "update cell parameters?" and "accept this solution?" questions. (If there is no reasonable solution, type "0" to reject all solutions and see "Problems" section below).
Use the "Predict" button to generate predicted diffraction pattern. If picked spots are confusing the display, use "Clear spots" to remove them; answer "y" to the "simply remove spots from display?" question. Predictions may be removed and replaced as often as desired using the "Clear predictions" and "Predict" buttons.
Check crystal mosaicity by comparing real and predicted spots along a lattice row. If there are extra predicted spots at the end of the row, the mosaicity being used is too high; if there are real spots which are not being predicted, the mosaicity used is too low. To estimate the correct value, change the "Mosaicity" field in the "Processing params" list and click "Predict" again. Repeat until predicted and real spots correspond as well as possible. For integration, use a mosaicity value slightly above this.
The effect on the predictions of changing other parameters than mosaicity may also be examined. For a parameter in the "Processing params" list, click on the old value, type in a new value, and hit C/R to store it. For a parameter not on the list, click "Keyword Input" to bring up a dialog window, type the parameter name and value (e.g. "SEPARATION 0.4 0.4"), hit C/R, then type "GO" to close the window and return control to the mosflm interface. Click "Predict" to see the prediction using the new parameters.
To continue after indexing, use the "EXIT" button to close the display window. A window will come up to ask "save current parameters?" If you answer "y" and accept the default file name, the unit cell, symmetry, wavelength, direct beam position, two theta, and distance will be passed to the main GUI; if you answer "n", or give another file name, you must manually transfer any needed information from the mosflm display to the windows of the main GUI. Note that any other parameters that you may have changed will not be transferred - you must modify settings for minimum spot separation, etc. manually. Answer "y" to the "exit?" question. In the "Xmosflm" window, run a strategy calculation if you wish (see "Strategy" section below). Then type "end" (the main GUI will be unresponsive until you have terminated mosflm).
MOSFLM => strategy Strategy option will be run in automatic mode. Speedup factor will be calculated automatically (use keyword SPEEDUP to set explicitly). Type GO to continue, or ABORT to stop strategy run. MOSFLM => go Default speedup set to 46.0 . . . Optimum rotation gives 97.8% of unique data This corresponds to the following rotation range(s): From 132.0 to 162.0 degrees Type "STATS" for full statistics. . . . STRATEGY =>Optionally type "stats" to get detailed statistics about completeness and redundancy over the calculated range. Type "end" to return to the "MOSFLM =>" prompt.
To get statistics for a particular range of spindle angles (for example, 0 to 90), do this:
MOSFLM => strategy start 0 end 90 MOSFLM => go Default speedup set to 46.0 . . . COMPLETE option =============== Give the segments of data to be tested, in the form: START 0 END 20 (RUN 1) . . . STRATEGY =>Enter the range of interest, which must be contained within the initial range given (0 to 90 in this case) as "start 0 end 45", for instance. Then type "go" to start the calculation. This sequence may be repeated for other ranges of angle. When done checking ranges, type "end" to exit strategy mode.
Exit from mosflm by typing "end" at the "MOSFLM =>" prompt.
Neither method uses spot positions to refine unit cell, mosaicity, and crystal orientation; they use the "post-refinement" approach of comparing calculated and observed intensities for partial reflections. For some sets of images, this approach does not give good results, and it is better to get the best possible indexing and proceed directly to integration. Generally, however, refinement is worth a try.
Refine: MOSFLM |
Mosflm refinement uses the "POSTREF SEGMENT" option. To do this, click "Refine:MOSFLM". In the Refinement Control window that comes up, select images for "Mosflm Refine". Pick two sets of 2-4 images separated by at least 10 degrees or so in phi (if available). Choose whether to refine mosaicity ("ISOTROPIC" selected - usually desirable) or not ("NONE" selected). The unit cell can be held fixed ("FIX CELL" selected), but this is seldom desirable (only if you are sure the current cell is correct and you want to check mosaicity and orientation).
Note for Fuji imaging plate (or other offline scanner) data - you must turn on "Edit Cmd File Before Execution" and supply direct beam positions for images to be used in refinement. See command file section for details.
Click "START REFINEMENT" to start up the actual refinement process. A window will pop up monitoring the log file which is being generated. If you want to take a close look at the log file during refinement, you can turn off window updating using the "Discontinue Logfile Updates of Screen" button; then use the scroll bar to move around in the file. To resume updating, use the "Resume Logfile Updates of Screen" button.
When refinement is complete, the log file window will show "**** END OF PROCESSING ****" for normal termination. Close the monitor window using the "CLOSE logfile display" button at the bottom. A summary of the results will appear in the "Results" panel of the "Refinement Control" window, and the message window on the main GUI will show the new matrix file.
If monitor window updating stops but "**** END OF PROCESSING ****" does not appear, something went wrong. Scroll back the text in the window to find the "*** FATAL ERROR ***" message describing the problem; scroll back farther to see details of the refinement process. Then close the monitor window and see "Problems" below for what to try next.
Normal output in Refinement Control window: |
---Cell--- Old: New: a : 56.023 56.144 b : 62.042 62.305 c : 128.946 129.495 alpha : 90.000 90.000 beta : 90.000 90.000 gamma : 90.000 90.000 ---Missetting Angles--- Old: New: Phi(X) : 0.000 -0.000 Phi(Y) : 0.000 -0.004 Phi(Z) : 0.000 0.074 ---Mosaicity--- Old: New: 0.100 0.128 ---Camera Constants--- Old: New: Beam Posn(X) : 94.901 94.910 Beam Posn(Y) : 93.269 93.280 Distance : 150.000 150.480 |
Normal output in main message window: |
. . . New matrix file: 0.00283417 0.00002406 -0.00707585 -0.01568842 0.00411693 -0.00117798 0.00449696 0.01434749 0.00034988 0.000 -0.004 0.074 0.17109932 0.00161176 -0.98525256 -0.94711274 0.27581346 -0.16402450 0.27148214 0.96120977 0.04871751 56.1442 62.3053 129.4947 90.0000 90.0000 90.0000 -0.0001 -0.0039 0.0742 Cell refinement finished. Results are in the log file: test_1_1_10_mosflm_refine.log |
Refined values for unit cell, missetting angles, mosaicity, and camera constants (for the last frame) are shown. For a successful refinement, changes in all parameters should be relatively small. If this is not so, there is a problem - see below for suggestions. If values look reasonable, clicking "Save Everything" will save them all. You can save subsets of values by clicking the appropriate buttons: "Save Mosaicity", "Save Unit Cell", "Save Misset Angles", "Save Beam Pos/Dist". For integration, it is usually safer to supply a value for mosaicity (in the main GUI window) slightly larger than the value from refinement. Unit cell parameters should be updated now unless they look unreasonable, as they are not generally refined during integration. Missetting angles and camera constants will usually be refined during integration, but should also be updated now if reasonable. Note that updating cell and/or angles alters the mosflm matrix file - you cannot get back to the original file except by indexing again.
If there are substantial changes in the unit cell or camera constants, you may want to do another pass of refinement. Save everything, or at least the new cell and beam position/distance (if mosaicity has gone negative, don't save that!), and hit "START REFINEMENT" again. After refinement, you can check the new predictions (using whatever new parameters you have saved): hit "Display Result" to bring up an "Xmosflm" window, type "@display.inp" in that window, and click the "Predict" button in the mosflm display window which appears. Check predictions for other images if you like (using "Read Image" and "Predict" buttons), then click "EXIT" and type "end" in the Xmosflm window.
"Usable reflections" are medium-to-strong partials extending across two frames. You can increase their number by adjusting the starting mosaicity (set it in the main GUI window and click "SAVE"), by changing the resolution range, or by changing the rejection parameters for refinement. For a highly mosaic or weakly diffracting crystal, it may not be possible to find sufficient usable reflections for mosflm refinement to work. Try postchk. Or, try very careful indexing followed directly by integration; it may be necessary to split up the frames into groups and index each group separately. DPS scaling can then be used to be sure all groups have the same indexing, and to refine crystal parameters.
Overlarge shifts could be due either to a bad initial indexing or to use of unsuitable images.
Postchk |
To perform Postchk refinement, first integrate 10-20 frames with no post-refinement: in "Integration Parameters", disable post-refinement. Set the starting and ending image numbers to include 10-20 frames. Then click "Integrate:Mosflm". A running display of the integration's progress will appear. When integration is complete, close the log file display and click "Postchk" to bring up the Refinement Control window. Select the frames for postchk (the ones you just integrated), and click "START REFINEMENT" to start the actual refinement.
Normal output in Refinement Control window: |
---Cell--- Old: New: a : 55.874 56.210 b : 62.026 62.410 c : 129.745 129.770 alpha : 90.000 90.000 beta : 90.000 90.000 gamma : 90.000 90.000 ---Missetting Angles--- Old: New: Phi(X) : 0.000 -0.305 Phi(Y) : 0.000 0.000 Phi(Z) : 0.000 0.012 ---Mosaicity--- Old: New: 0.100 0.120 |
Normal output in main message window: |
. . . DISTRIBUTION OF CALCULATED-OBSERVED FRACTIONS PACKS PHIS PHIE NREF PHIX PHIY PHIZ ETA A B C rmsr -5 -2 2 5 1- 10 1.00 9.00 1081 -0.145 0.001 -0.038 0.04 55.86 62.39 130.37 0.04 461 174 539 227 107 Postchk finished. |
Refined values for unit cell, missetting angles, and beam mosaicity are shown. For a successful refinement, changes in cell and mosaicity should be relatively small. Missetting angles determined by postchk are inaccurate, particularly if the images used cover a wide range of spindle angles, and shifts of several tenths of a degree do not necessarily indicate a problem. If results look reasonable, save the cell parameters ("Save Unit Cell"). Save mosaicity ("Save Mosaicity"), or (preferably) update the value in the main window to be slightly larger than the refined value. Use "Display Result" button to see predictions using refined parameters, as for mosflm refinement.
If postchk completes, but changes in cell parameters or mosaicity are unreasonable, check for problems with integration, as above. If none are found, try saving the new cell and integrating the same set of 10-20 frames, with post-refinement of orientation only, or no post-refinement. If this succeeds, go ahead and process the full set. If not, try mosflm refinement, or integration with no refinement.
Integrate: Mosflm |
Integration is carried out with mosflm. The principal integration parameters are set using the GUI. Other parameters normally default to reasonable values; they can be changed in unusual cases, as described below. Important parameters include:
If you need to change other parameters in this group, use the mosflm on-line help facility (type "help" at the MOSFLM => prompt in an Xmosflm window) for an explanation of their significance.
Mosaicity may be refined ("Mosaicity Refinement: ISOTROPIC" selected), particularly if the real crystal mosaicity is anisotropic or varying in time. A reasonably constant mosaicity is also a check on the good behavior of the post-refinement. "Start Mos for Frame: CURRENT" means that the initial divergence for each frame is set to the refined value for the previous frame. Only set this if the refinement is very well behaved and you expect a substantial drift in divergence with time. "Start Mos for Frame: INITIAL" begins the refinement for each frame with the original value; this is usually preferred.
To refine unit cell parameters, set "Fix Cell?" to "NO". These parameters are refined for a group of images rather than a pair, where the "Width" parameter specifies the number of frames in the group. The "Maxresid" and "Maxshift" parameters tell how much change in the cell parameters is acceptable, and "Repeat" specifies the maximum number of times that refinement of a group will be repeated in an attempt to converge on sensible values.
Each "batch number" in the output file is given by the image number plus the offset. The offset is normally 0, but should be set to some positive value if multiple runs with overlapping image numbers are to be merged; batch numbers of all batches to be scaled together must be unique.
Click "Integrate:Mosflm". The "Integration Parameters" window comes up, so you can check the current parameter values. Then click "START INTEGRATION" to proceed. If you are editing the command file, it will come up in a window now. Make changes and exit the editor.
When you start integration, a monitor window comes up to follow the output to the log file which is being generated (test_1_1_10_mosflm.log, e.g.). When integration completes normally, the monitor window will show the "**** END OF PROCESSING ****" message from mosflm, followed by output file header information. A summary of the results will appear in the main GUI window:
. . . IMAGE CCX CCY CCOM DIST YSCALE TILT TWIST ROFF TOFF RESID WRESID F P O N B I/sig(I) I/sig(I)_outer Rsym Nsym SDRAT $$ $$ 1 0.01 0.01 0.01 151.4 1.000 -13 2 0.00 0.00 0.021 1.3 1313 919 47 52 0 32.6 7.0 0.036 724 2.7 2 0.01 0.01 0.01 151.5 1.000 -17 4 0.00 0.00 0.021 1.0 1322 854 47 53 0 32.8 6.8 0.043 392 2.9 3 0.01 0.01 0.01 151.5 1.000 -15 3 0.00 0.00 0.021 1.4 1367 811 38 69 0 33.0 6.8 0.039 254 3.3 4 0.01 0.01 0.01 151.5 1.000 -16 3 0.00 0.00 0.020 1.1 1289 936 34 63 0 32.7 7.0 0.043 174 3.4 5 0.01 0.01 0.01 151.5 1.000 -18 4 0.00 0.00 0.020 1.2 1339 964 41 68 0 32.6 7.0 0.035 146 3.0 6 0.01 0.01 0.00 151.4 1.000 -16 7 0.00 0.00 0.020 1.3 1345 938 43 74 0 31.5 6.6 0.036 104 2.8 7 0.01 0.01 0.00 151.4 1.000 -15 6 0.00 0.00 0.023 1.4 1358 965 43 86 0 31.3 5.7 0.044 106 3.1 8 0.01 0.01 0.00 151.4 1.000 -14 2 0.00 0.00 0.020 1.3 1394 979 36 79 0 30.5 6.6 0.047 92 3.4 9 0.01 0.01 -0.01 151.5 1.000 -15 4 0.00 0.00 0.021 1.3 1410 944 30 91 0 30.0 7.0 0.056 80 2.7 10 0.00 0.01 -0.01 151.4 1.000 -20 3 0.00 0.00 0.023 1.3 1462 974 36 79 0 28.3 6.2 0.058 66 2.6 $$ $TABLE: Post refinement: $GRAPHS :Missets phix phiy phiz v image:A:1,2,3,4: :Cell parameters A,B,C v image:A:1,5,6,7: :Cell angles alpha beta gamma v image:A:1,8,9,10: :Mosaic spread v image:A:1,11: :Beam divergences v image:A:1,12,13: $$ Image PHIX PHIY PHIZ A B C ALPHA BETA GAMMA MOSAIC DIVH DIVV Resid NR $$ $$ 1 0.00 0.03 0.06 56.29 62.50 130.16 90.00 90.00 90.00 0.14 0.10 0.02 0.010 315 2 0.00 0.03 0.05 56.29 62.50 130.16 90.00 90.00 90.00 0.13 0.10 0.02 0.007 269 3 0.00 0.03 0.05 56.29 62.50 130.16 90.00 90.00 90.00 0.12 0.10 0.02 0.009 278 4 0.00 0.02 0.05 56.29 62.50 130.16 90.00 90.00 90.00 0.13 0.10 0.02 0.009 359 5 0.00 0.01 0.05 56.29 62.50 130.16 90.00 90.00 90.00 0.13 0.10 0.02 0.010 288 6 0.00 0.01 0.05 56.29 62.50 130.16 90.00 90.00 90.00 0.12 0.10 0.02 0.010 312 7 0.00 0.00 0.05 56.29 62.50 130.16 90.00 90.00 90.00 0.12 0.10 0.02 0.008 315 8 0.00 0.00 0.05 56.29 62.50 130.16 90.00 90.00 90.00 0.12 0.10 0.02 0.009 295 9 0.00 -0.01 0.05 56.29 62.50 130.16 90.00 90.00 90.00 0.13 0.10 0.02 0.010 289 $$ Mosflm finished. Please examine the information printed to the screen from the summary file; also examine the log file: test_1_1_10_mosflm.log Sorting results Sortmtz finished. |
The summary shows the refined values of the camera constants for each frame and also the results of post-refinement (if enabled). Check for reasonable and consistent values. For more detailed information, examine the log file, by looking in the log file monitor window or using an editor or xloggraph. When done with the monitor, close it using the "CLOSE logfile display" button.
Failures can occur during:
Scaling:DPS |
The DPS scaling program is a new program written by Robert Bolotovsky at Purdue. Important features include:
Click on "Scaling:DPS" to bring up the "Scaling Parameters" window. Important parameters include:
Each line in the "Definitions of runs" table defines one run. You may specify the input file either by its name or by image prefix, run number, start number, and end number. In the latter case, the file name will be constructed from the other items.
If the "Start no." and "End no" fields are blank, all frames in the file will be used. If not, the specified range of batch numbers (frame number plus offset) will be used. The same input file may be specified multiple times with different ranges of batch number; these ranges must not overlap. Ranges from different files may overlap without confusion, as the program will assign a unique internal sequence number to each frame.
"Explicit" reindexing allows you to specify any transformation of indices you want: in the "Explicit reindexing parameters" window of "Still More Parameters", define groups by filename and batch number range; define transform as new indices, e.g. "-h -k l" for a 2-fold rotation about c*; enter "Y" or "N" under "Mat?" for whether or not to update the orientation matrix as well as the indices.
Output from DPS scaling goes to a log file (test_1_dps_scale.log, for example), which is monitored during the run. Xloggraph can be used to make various useful plots of the results.
Scaling can have various problems, including:
Scaling:SCALA |
Scala is a versatile scaling program from the CCP4 suite. Click on "Scaling:SCALA" to bring up the "Scaling Parameters" window.
Important parameters include:
Each line in the "Definitions of runs" table defines one run. You may specify the input file either by its name or by image prefix, run number, start number, and end number. In the latter case, the file name will be constructed from the other items, so the integration run that produced the file must have used the default output file name, and a batch number offset of 0.
If the "Start no." and "End no" fields are blank, all frames in the file will be used. If not, the specified range of batch numbers (frame number plus offset) will be used. The same input file may be specified multiple times with different ranges of batch number; these ranges may not overlap. Be sure all batch numbers to be scaled together are unique.
Output from scala goes to a log file (test_1_scala.log, for example), which is monitored during the run. When the run is complete, it is advisable to examine the log file using xloggraph, a program from CCP4 that allows for generating plots from tabular information in the file, as well as displaying the file itself.
Full documentation is available as part of the CCP4 documentation set.
Scaling can fail for various reasons, including:
I to F: Truncate |
DPS scaling produces an ASCII file of scaled and merged intensities, which can go directly into a phasing program.
When scala is used, its output is an MTZ file containing scaled and merged intensities. To produce final files of F's, in both binary (MTZ) and ASCII formats, click on the "I to F:Truncate" button. The programs used are truncate and mtz2various, from CCP4. There is normally no need to change any parameters from the defaults, but if necessary it can be done by editing the command file.
The control file may be edited to change the flow of operations resulting from activation of a button on the GUI. This is seldom necessary. Individual command files, however, may be edited routinely to change processing parameters which have no representation in the GUI windows.
The first part of Mosflm_control.com looks like this:
#!/bin/csh -f # set PARAM_FILE = $1 set OPTION = $2 # set CWD = `get_gdb $PARAM_FILE Working_Dir` ^ set EDIT_SCRIPT = `get_gdb $PARAM_FILE Edit_Script` | <= Part 1 set IMAGE_PREFIX = `get_gdb $PARAM_FILE Image_Prefix` V echo "Running option: $OPTION" if("$EDIT_SCRIPT" == "1") then ^ set user_editor = `printenv GUI_EDITOR` | if ("$user_editor" == "") then | <= Part 2 set user_editor = "vi" | endif | endif V # cd $CWD goto $OPTION # Indexing: ^ # | echo "Running autoindexing interactively with Mosflm" | if ( "$EDIT_SCRIPT" == "1") then | set editor_result = `xterm -geom 80,24 -title MosflmIndex.com -e $user_editor MosflmIndex.com` endif | <= Part 3 | csh -v MosflmIndex.com $PARAM_FILE ${DISPLAY} | exit VThis code includes (1) extraction of some values from the parameter file, (2) selection of an editor based on the GUI_EDITOR environment variable, and (3) execution of the (mosflm) Indexing option. The rest of the command file includes sections for the other options.
Here is part of the command file for DPS indexing:
# set PARAM_FILE = $1 ^ # | set run_no = `get_gdb $PARAM_FILE Run_Number` | set name = `get_gdb $PARAM_FILE Image_Prefix` | set StartImNo = `get_gdb $PARAM_FILE Start_Image_Number` | set EndImNo = `get_gdb $PARAM_FILE Last_Image_Number` | set file_dir = `get_gdb $PARAM_FILE Image_Dir` | set resolution = `get_gdb $PARAM_FILE Resolution` | <= Part 1 set beam = `get_gdb $PARAM_FILE Beam_X Beam_Y` | set wavelength = `get_gdb $PARAM_FILE Wavelength` | set distance = `get_gdb $PARAM_FILE Distance` | set twotheta = `get_gdb $PARAM_FILE Twotheta` | set deltaphi = `get_gdb $PARAM_FILE Delta_Phi` | set StartAngle = `get_gdb $PARAM_FILE Start_Angle` | set lattice_name = `get_gdb $PARAM_FILE Lattice_Name` | set cell_max = `get_gdb $PARAM_FILE DPS_Longvec` | set low_res = `get_gdb $PARAM_FILE DPS_Lowres` | set high_res = `get_gdb $PARAM_FILE DPS_Highres` | set spindle_dir = `get_gdb $PARAM_FILE Spindle_dir` | set spindle_vert = `get_gdb $PARAM_FILE Spindle_vert` | set crystal_system = `get_gdb $PARAM_FILE Crystal_System_Name` | set detector = `get_gdb $PARAM_FILE Detector_Type` | set suffix = `get_gdb $PARAM_FILE File_Suffix` | set use_target = `get_gdb $PARAM_FILE DPS_Use_Target` | set target_cell = `get_gdb $PARAM_FILE DPS_Target_Cell` | | if ("${run_no}" != "") then | set long_name = "${name}_${run_no}" | else | set long_name = "${name}" | endif V . . . # set st_3dig = `make_3digit $StartImNo` ^ # | # Check first image. | # | set first_img = ${file_dir}/${long_name}_${st_3dig}.img | <= Part 2 if(-e ${first_img}) then | goto first_img_ok | endif V # first_img_ok: # . Part 3 . | . V switch ("$detector") case ADSC_Quantum: case R-axis: case MAR: case MAR_IP: case MAR_CCD: set rsizef_head = `mh_st rastersize1 ${detector} < ${first_img}` set rsizes_head = `mh_st rastersize2 ${detector} < ${first_img}` set imsizef_head = `mh_st imsize1 ${detector} < ${first_img}` set imsizes_head = `mh_st imsize2 ${detector} < ${first_img}` if (${rsizes_head} != '0.0000') then if (${rsizes_head} != ${rastersizes}) then echo "**** Warning - rastersize ${rastersizes} in parameter file disagre es with value ${rsizes_head} in file header." echo " File header value is used." set rastersizes = ${rsizes_head} endif endif . . . if ($wavelength == '0.0000') then set wavelength = \ `mh_st wavelength ${detector} < ${first_img}` echo "Wavelength set to ${wavelength}, from file header." set status = `put_gdb $PARAM_FILE Wavelength ${wavelength}` else set wave_head = \ `mh_st wavelength ${detector} < ${first_img}` if (${wave_head} != ${wavelength}) then echo "**** Warning - wavelength ${wavelength} in parameter file disagree s with value ${wave_head} in file header." echo " Parameter file value is used." endif endif . . . set raster_rs = `mos2dps_coord $detector $beam $rastersizef $rastersizes $imsizef $imsizes` # # If direct beam position from adxv doesn't match either parameter file # or file header, get new value # if (-e ${file_dir}/.adxv_beam_center) then ^ if (-w ${file_dir}/.adxv_beam_center) then | if (-e .old_beam_center) then | /bin/rm temp_center | cp ${file_dir}/.adxv_beam_center temp_center | echo " " >> temp_center | diff -b temp_center .old_beam_center > DIFF_FILE | if (-z DIFF_FILE) then | /bin/rm DIFF_FILE | /bin/rm temp_center | else | if (-e .header_beam_center) then | /bin/rm temp_center | cp ${file_dir}/.adxv_beam_center temp_center | echo " " >> temp_center | diff -b temp_center .header_beam_center > DIFF_FILE | if (-z DIFF_FILE) then | <= Part 4 /bin/rm DIFF_FILE | /bin/rm temp_center | else | while (-e ${PARAM_FILE}.lock) | sleep 3 | end | touch ${PARAM_FILE}.lock | set raster_rs = \ | `adxv2dps_coord ${file_dir}/.adxv_beam_center ${PARAM_FILE}` echo `adxv2mos_coord ${file_dir}/.adxv_beam_center ${PARAM_FILE}` echo "Direct beam position reset to $raster_rs" | /bin/rm DIFF_FILE | /bin/rm temp_center | endif | /bin/rm .header_beam_center | else | while (-e ${PARAM_FILE}.lock) | sleep 3 | end | touch ${PARAM_FILE}.lock | set raster_rs = \ | `adxv2dps_coord ${file_dir}/.adxv_beam_center ${PARAM_FILE}` echo `adxv2mos_coord ${file_dir}/.adxv_beam_center ${PARAM_FILE}` echo "Direct beam position reset to $raster_rs" | /bin/rm ${PARAM_FILE}.lock | /bin/rm DIFF_FILE | /bin/rm temp_center | endif | endif | /bin/rm .old_beam_center | endif | endif | endif V # set dps_2th = `mulf $twotheta '-1.0'` . . . /bin/rm control_index ^ | if ($use_target == '1') then | echo "mode target_cell" > control_index | else | echo "mode automatic" > control_index | endif | echo "##parameter_file $PARAM_FILE" >> control_index | echo "resolution ${low_res} ${high_res}" >> control_index | echo "cell ${cell_max}" >> control_index | echo "wavelength ${wavelength}" >> control_index | echo "rastersize ${rastersize}" >> control_index | <= Part 5 echo "distance ${distance}" >> control_index | echo "twotheta ${dps_2th}" >> control_index | echo "beamstop ${raster_rs}" >> control_index | echo "film_rotation ${film_rotation}" >> control_index | echo "sscale $y_scale" >> control_index | echo "peaks peaks.file 0.0 ${deltaphi}" >> control_index | echo "omfile ${long_name}.om" >> control_index | # | dps_index < control_index > dps_index.log1 | /bin/mv PEAKS_WITH_PHIS NEW_PEAK_FILE V if(-e POST_ERROR) then ^ echo "dps_index: FAILED. SKIP FURTHER INDEXING PROGRAMS." | exit | endif | | <= Part 6 /bin/rm PEAKS_WITH_PHIS | /bin/rm NEW_PEAK_FILE | dps_analyseOM ${name}_${run_no}.om analyze.log | dps_bravais < control_bravais > bravais.log V . . . #This includes (1) extraction of values from the parameter file, (2) a check for existence of a data file, (3) extraction of values from an image file header (if there is one; choices are made based on detector type as to what can be obtained from the file header), (4) getting the direct beam coordinates from another file, (5) construction of a control file and execution of the indexing program, and (6) execution of a series of secondary programs.
When the "Edit Cmd Files Before Execution" button on the main GUI window is on, there will be an opportunity to edit each command file before it is executed. An xterm window will appear, with the file open in the editor selected by the GUI_EDITOR environment variable. If GUI_EDITOR is not set, "jot" will be used on SGI machines and "vi" on others. Use the editor to alter the file and save it. When you exit from the editor, the script will be executed. As the updated command file overwrites the original one in this process, any changes made will stay in effect for future runs, unless you use the "Copy Cmd Files" button to reload the standard files.
To change a processing parameter, find the place in the command file where it is being written to a control file and alter the write statement as necessary. You can make other changes in a command file, as long as the result is a valid shell script, but this will not generally be necessary.
Mosflm command lines for "Refine:MOSFLM" that can be changed only by editing the command file "MosflmRefine.com" include:
"SYNCHROTRON POLAR 0.89" "DISPER 0.0025" Polarization and dispersion of the x-ray beam "LIMITS RMIN 5 RMAX $rmax YMAX $rmax XMAX $rmax xscan $rmax yscan $rmax" "BACKSTOP RADIUS 5 CENTRE $beam" Beam stop radius and position, and low resolution limit "NULLPIX ..." Detector parameter "REFINEMENT CYCLES 2 FIX YSCALE RESID 15 IMIN 20 5 NSIG 6" "REFINEMENT INCLUDE PARTIALS 0.5" "REFINEMENT LIMIT $ref_limit" Parameters for refinement of camera constantsThe refinement parameters are the ones most likely to need changing. The default values specify:
LIMITS EXCLUDE 10.0 25.0 40.0 50.0
where the two pairs of numbers specify the upper left and lower right corners of a rectangular area to be excluded from processing. The coordinates are in mm. and are relative to the scan origin. Multiple areas may be specified, up to a maximum of 10.
PROCESS 1 TO 3 ADD 0 START 0.0 ANGLE 1.0
becomes:
BEAM 111.3 100.5 PROCESS 1 TO 1 ADD 0 START 0.0 ANGLE 1.0 BEAM 110.3 102.3 PROCESS 2 TO 2 ADD 0 START 1.0 ANGLE 1.0 BEAM 112.2 101.6 PROCESS 3 TO 3 ADD 0 START 2.0 ANGLE 1.0
Mosflm command lines for "Integrate:Mosflm" that can be changed only by editing the command file "MosflmIntegrate.com" include all those listed above for refinement plus those created by the following lines:
set pr_0 = {"POSTREF SDFAC 3 SHIFTFAC 10.0 BEAM "}{$sw_beamtyp}{" USEBEAM FIX ALL"} set pr_1 = {"POSTREF MAXRESID "}{$pref_resid}{" MAXSHIFT "}{$pref_shift}{" WIDTH "}{$pref_width}{" REPEAT "}{$pref_rep} . . . set prof_line_0 = "PROFILE OPTIMIZE" set prof_line_1 = {"PROFILE BOUNDARY "}{$p_bound}{" RATIO "}{$p_ratio}{"TOLERANCE "}{$p_tol}{" RMSBG 10."} . . . MATRIX ${name}_$run_no.mat $pr_0 Post-refinement control $pr_1 $prof_line_0 Profile parameters $prof_line_1 PROCESS $StartImNo to $EndImNo ADD $add_no START $StartAngle ANGLE $deltaphi BLOCK $m_blockMost of the parameters on these lines can be set using the GUI, except for:
file_001.img 110.3 100.7 file_002.img 111.6 99.8 . . .These beam positions are in mosflm coordinates - determine them by using the mosflm display, or with some other program such as getbeam (available from MacCHESS). Name the file "prefix_start_end.beam", or "prefix_run_start_end.beam" if "Run No." is not blank, where prefix is the image prefix, start is the first frame number of the series to be integrated, and end is the last frame number.
Some parameters used for merging, and for producing statistics, for DPS scaling can only be changed by editing the command file.
The only command line supplied to scala which can not be changed from the GUI is:
SDCORRECTION 1.25 0.03This gives correction factors for sigmas; other values may be more appropriate for some data sets.
Some other settable parameters have their default values. For information on them, see the scala documentation.
At present, parameters for final output can be changed only by editing the command file.
The standard truncate parameters are:
ANOMALOUS YES TRUNCATE YES FALLOFF YES LABOUT F(+)=F(+) SIGF(+)=SIGF(+) F(-)=F(-) SIGF(-)=SIGF(-)
These specify: output anomalous differences (if they are present in input), convert I's to F's using the "truncation" procedure of French and Wilson, check for anisotropy in falloff of intensity with resolution, label output columns F(+), SIGF(+), etc. To merge anomalous pairs, use "ANOMALOUS NO". To use F = SQRT(I), set "TRUNCATE NO". See CCP4 documentation for other options.
For help on mosflm, read "mosflm_user_guide.doc", in the /use/ccp4/mosflm directory on MacCHESS Alphas. Also, whenever an Xmosflm window is up, you can access mosflm interactive help by typing "help".
CCP4 documentation is available.
Help on the adxv display program is available using the "Help" button on the menu bar of each of its windows.
See the "Problems" section for descriptions of some miscellaneous problems that may occur when executing processing_gui.
June 2, 2000