Development of the software is continuing. This documentation is for Version 2.01, released August 2001. 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, you will probably use only a subset of the complete set of frames (as specified in the indexing and refinement windows); "sequence" gives the range that will be integrated.
Area (4) contains a few basic parameters for this dataset. Other general 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 and direction of spindle rotation 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. The display and strategy steps are optional; an image display is produced automatically at various stages, and the strategy calculation is only useful when preliminary processing is done prior to data collection.
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 (but often gives more accurate results with multiple images). Mosflm indexing gives the options of DPS or REFIX indexing. DPS indexing via mosflm 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 file specified by the "Images" (directory), "Image Prefix", "Run No.", "Start Image No.", and "Filename suffix" (in the "Detector Parameters" window) fields. The filename is of the form "prefix_run_startno.suffix" (run number given) or "prefix_startno.suffix" (run number field blank), where "startno" must be 3 digits long. If the file does not exist in the image directory, an error message will appear in the message window. Following the check, the appropriate window is brought up - see details below for the individual indexing programs. Indexing determines the unit cell and orientation of the crystal - these are stored in a mosflm-format matrix file, and the unit cell is also kept in the parameter file. If you know the unit cell very well and it differs slightly from the one determined by indexing, you can force a change by entering the desired cell in the "Cell Parameters" window and clicking "Update orientation matrix with this cell". This only works for small cell changes - you cannot swap axes or change symmetry this way.
After indexing, proceed to refinement.
| Index: DPS |
DPS indexing is a Fourier-based procedure which searches for periodicities along directions in reciprocal space. It 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 No." 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 dps_display to find and display peaks (shown as blue diamonds) for the first image. The default set of peaks found will be appropriate for most images, but if it is not you can use the "Peaks" option of the dps_display "Edit" menu to bring up a window showing the peak search parameters: change as needed and use "Find peaks" to get a new set of peaks. In difficult cases it may be necessary to manually add or remove peaks; turn on the appropriate toggle button and use the mouse to select peaks. 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 frame(s) other than the first, change the display to each of the other frames in turn by typing the new frame number in the "Frame:" field, or by using the up and down arrows to step one frame at a time. As long as the "Peaks" toggle button is on, new peaks will be automatically calculated whenever a new frame is loaded. 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.
The grayscale for image display can be changed using the sliders to the right of the "Predictions" button: adjust the left slider to change the bottom of the white-to-black range and the right slider to change the top of the range.
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. Change the magnification in the zoom window using the text field and/or arrows at the top of the window. If the cross is not centered on the spot, click on the correct position with the middle mouse button. Confirm the new position in the window that pops up. Note - the new coordinates will be written to the current parameter file but to update the "Machine Parameters" window you must click "LOAD" on the main GUI. Failure to click "LOAD" will result in the beam position being reset to the old values.
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, but don't expect any very long ones, the default value of 300 is a good place to start. 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". After dps_index completes its run, 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
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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
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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
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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. In addition, a display of predicted reflections for the first image using that solution will be produced. In the display, fully-recorded reflections are green, partials are yellow, and overlapping reflections are red. Partiality is determined using the current mosaicity (in the main GUI window) and overlaps are determined using the current minimum spot separation (in the Integration Parameters window, which pops up when you click "Integrate:MOSFLM"). To change to a different symmetry, click on the appropriate entry. This will update the symmetry entries in the parameter file and the Cell Parameters window, and display predictions using the new cell. To save the results from autoindexing directly to a matrix file (whether or not you have changed symmetries), click "Save result without refining" (in the Autoindexing window). To do some refinement before writing a matrix file, click "Refine result (DPS refine)". If you do a direct save now, you will still be able to refine later.
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 6.10 has two indexing options; the "new" indexing uses the same basic algorithm as dps_index, but your results may differ from those of "Index:DPS" due to differences in the peak search routine and in the "pre-refinement" of a few parameters that mosflm does after indexing.
The alternative "old", or "REFIX", or "Kabsch", option uses a different algorithm based on assigning inter-peak vectors to reciprocal space basis vectors. It 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 mosflm for indexing, 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 orientation differs from that in dps_display; the spindle rotation axis is horizontal in the dps_display display but 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. For DPS-style indexing, a single image can be used but two or three will usually give a better result. 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. If desired, repeat "Read image" and "Find spots" for additional frame(s). Then click "Autoindex".
In the window that comes up when "Autoindex" is activated, answer "y" or "n" to "use new indexing?", depending on whether you want DPS or Kabsch indexing. Then answer a few more questions; generally the default values are fine. 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". (If there is no reasonable solution, type "0" to reject all solutions and see "Problems" section below). A little more processing will be done and you will be asked whether to accept the results. The dialog above is from a Kabsch indexing run; the sequence is slightly different for DPS indexing, but in both cases the final question is "accept this solution?". If you answer "no", you will have a chance to reindex with different spot-selection criteria. If "yes", a matrix file containing cell and orientation information will be written.
Use the "Predict" button to generate a 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
Output from the strategy option looks like this:
Default speedup set to 46.0
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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.
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STRATEGY =>
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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
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COMPLETE option
===============
Give the segments of data to be tested, in the form:
START 0 END 20 (RUN 1)
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STRATEGY =>
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To get information about appropriate oscillation widths for your frames, you can use the TESTGEN option:
MOSFLM => testgen start 0 end 90
MOSFLM => go
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TESTGEN OPTION
==============
Generating from phi = 0.00 (START) to 90.00 (END) testing overlaps
every 5.00 degrees (STEP).
At each phi value, the oscillation angle which results in less than
0.0% overlaps (OVERLAP) will be determined, subject to a minimum oscillation
angle of 0.20 degrees (MINOSC) and a maximum of 5.00 (MAXOSC)
Testing at phi 0 degrees
Testing at phi 5 degrees
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Suggested data collection stratgey for a maximum spot overlap of 0.0%
Phi start Phi end no of images oscillation angle %age overlaps %age fulls
0.0 5.0 10 0.50 0.0 23.8
5.0 9.9 9 0.55 0.0 23.8
9.9 19.7 15 0.65 0.0 32.3
19.7 24.9 7 0.75 0.0 37.5
24.9 34.7 15 0.65 0.0 31.4
34.7 44.9 12 0.85 0.0 43.8
44.9 50.1 5 1.05 0.0 50.7
50.1 54.9 5 0.95 0.0 46.8
54.9 65.1 12 0.85 0.0 41.5
65.1 74.9 28 0.35 0.0 8.0
74.9 84.8 2 4.95 0.0 86.6
84.8 90.8 7 0.85 0.0 42.2
***** IMPORTANT *****
The suggested values depend critically on the estimates of mosaic spread
and the SEPARATION parameters. These values MUST be realistic, or you may
not end up with a complete dataset.
In particular, the spot separation parameters should be at least as large
as the spot size in the centre of the image.
Current values: Mosaic spread 0.11 Spot separation 0.60 0.60mm
These are the MAXIMUM possible oscillation angles.
A better signal to noise may be achieved by using a smaller oscillation
angle if the oscillation angles suggested are greater than the rocking width
(mosaic spread plus beam divergence)
MOSFLM =>
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To start refinement, use either the "Refine result (DPS refine)" button in the "Autoindexing" window or the "Refine" button on the main GUI. Select the desired program in the "Refinement Control" window, select the items to be refined and the frames to be used, and click "START REFINEMENT". Follow refinement progress by watching the message window of the main GUI, which monitors the log file being generated by the process. When refinement is complete, new parameter values appear in the "Results:" area of the Refinement Control window, and dps_display is started to show new predictions for the first image. Refined parameter values are saved to the parameter and matrix files when you click one of the "Save" buttons - usually "Save Everything", but it is possible to save a subset of the refined parameters. Refinement can be repeated as often as desired: after saving refined parameters, change options (program to use, parameters to refine, frames to use) if desired, click "START REFINEMENT" again. When you are satisfied with the results, use "CLOSE" to close the Refinement Control window and proceed to integration.
Note that for integration it is wise to reset the mosaicity (on the main GUI window) somewhat higher than the final refined value, to allow for residual errors in cell and orientation parameters, and for anisotropy in mosaic spread.
Details for the three refinement options are given below.
| Refine (dps_refine) |
Dps_refine follows the Rossmann approach of cyclic refinement of the "Q" and "A" matrices, followed by a final step of mosaicity estimation. The Q-matrix incorporates information on beam position, distance, and detector rotations, while the A-matrix depends on unit cell and crystal orientation. Shifts in Q-matrix elements, and in cell parameters, depend on the discrepancy between observed and calculated spot positions. Crystal orientation, however, is adjusted to maximize the total integrated intensity of all reflections.
Single or multiple frames may be used. The program default for "Frames to use in refinement" is the first frame only, but better results may be obtained using several frames, e.g. "1 5 10". Typically, frames used should range over 10-30 degrees in phi; a larger range gives more information on cell parameters, but if the range is too large the initial indexing may not be good enough to locate spots on some frames.
The current algorithm used by dps_refine for mosaicity estimation is unsatisfactory - you will do better to refine mosaicity using mosflm (if possible) or just estimate it by comparing observed and predicted spot patterns. The recommended initial set of items to refine is "Unit Cell", "Xtal Orientation", and "Beam/Distance". On later cycles, "Detector Rotns" may also be refined.
Note - for Fuji imaging plate (or other offline scanner) data - you can only use one image, as there is currently no provision for providing multiple direct beam positions and detector rotations.
Click "START REFINEMENT" to start up the actual refinement process. If you want to take a closer look at the log file during refinement, you can turn off window updating using the "Pause" button in the corner of the message window; then use the scroll bar to move around in the file. To resume updating, use the "Resume" button.
When refinement is complete, the log file window will show a series of matrices, followed by "Done.", for normal termination. A display of the new predictions for the first image will be presented, and a summary of the results will appear in the "Results:" panel of the "Refinement Control" window.
If "Done." does not appear, something went wrong. Scroll back the text in the window to find the error message describing the problem; then see "Problems" below for what to try next.
If refinement is successful, predicted reflections on the display should match actual spots better than before refinement. Changes in unit cell and detector parameters should be relatively small.
The missetting angles sometimes look very large even when refinement is successful, due to the fact that dps_refine works with a set of primitive vectors which do not always correspond to the standard ones defining the cell. When these vectors are used to generate a final orientation matrix, the program sometimes comes up with a matrix related by a symmetry transformation to the original one. This annoying "feature" will be fixed in a future release. As long as predicted spots match real ones better than before refinement, the refinement has succeeded.
Check new predictions for other frames by changing the "Frame:" field in the display window. If predictions match real spots worse than before, or parameter changes are unreasonable, there is a problem - see below for suggestions. If values look reasonable, clicking "Save Everything" will save them all (any parameters that were not being refined will be unaffected). This is usually the right thing to do, but if necessary you can save subsets of values by clicking the appropriate buttons: "Save Unit Cell", "Save Misset Angles", or "Save Beam/Distance".
Note that updating cell and/or angles alters the orientation matrix file - you cannot get back to the original file except by indexing again.
If parameter changes are much different from zero (except for the missetting angles, as mentioned above), you should probably do another round of refinement. Save everything, and hit "START REFINEMENT" again. You can repeat the "Save" - "START" sequence as often as needed, until parameter changes are negligible. If you used only one frame for the initial refinement, or were keeping some parameters fixed, you may want to add more images or refine more parameters for later cycles. If refinement has converged to a reasonable looking set of parameters, that predict spot positions well, you are ready to proceed to integration.
"Usable reflections" are those above a minimum I/sigma(I) value. You can increase their number by including more frames, and/or by changing the resolution range and/or mosaicity (set the latter two in the main GUI window and click "SAVE"). If a continuous sequence of frames is available, you may have better luck with mosflm or 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.
If refinement completes but parameter changes are large:
| Refine (mosflm) |
Mosflm refinement uses the "POSTREF SEGMENT" option, which works by comparing calculated and observed intensities for partial reflections. Camera constants (beam position, distance, and detector rotations) are refined for each individual frame, after which information from all specified frames is used to refine unit cell, crystal orientation, and mosaicity.
The process requires one or two sets of 2-5 consecutive images. Two sets separated by 10-30 degrees in phi are usually suitable. Designate the sets in the "Frames to use in refinement" field, e.g. "1-3 28-30". Initially, the program will set the field to specify the first 3 and last 3 frames in the range from "Start Image No." to "End Image No.". If the total range is large, it is better to use a second segment only about 20 degrees away from the first, or else mosflm may be unable to locate reflections in the second segment from the initial orientation matrix. If the initial indexing is not very good, you may need to use only a single segment close to the frame(s) used for indexing, e.g. "1-5".
With good images and low to moderate mosaicity, mosflm can do a good job of refining all parameters, and all items in the "Refine:" list should be selected. If mosaicity is high, i.e. greater than about 1.5 times the oscillation width, it will not refine well and should be held fixed. If you know the unit cell or direct beam position and distance very well, you may want to keep them fixed. It may also be necessary to keep the cell fixed if only a small range of spindle angle is covered by the frames, particularly if symmetry is low. Unless you know that mosaicity is too high to be refined, a good approach is to first try refining everything. If results are poor, then try rerunning with some parameters fixed.
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. If you want to take a closer look at the log file during refinement, you can turn off window updating using the "Pause" button in the corner of the message window; then use the scroll bar to move around in the file. To resume updating, use the "Resume" button.
When refinement is complete, the log file window will show "**** END OF PROCESSING ****" for normal termination, followed by the new matrix file. A display of the new predictions for the first image will be presented, and a summary of the results will appear in the "Results:" panel of the "Refinement Control" window.
If a new matrix file 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 see "Problems" below for what to try next.
If refinement is successful, predicted reflections on the display should match actual spots better than before refinement, and changes in crystal and detector parameters should be relatively small. Check new predictions for other frames by changing the "Frame:" field in the display window. If predictions match real spots worse than before, or parameter changes are unreasonable, there is a problem - see below for suggestions. If values look reasonable, clicking "Save Everything" will save them all (any parameters that were not being refined will be unaffected). This is usually the right thing to do, but if necessary you can save subsets of values by clicking the appropriate buttons: "Save Unit Cell", "Save Mosaicity", "Save Misset Angles", "Save Beam/Distance", or "Save Detector Rotns".
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 parameter changes are much different from zero, you should probably 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. You can repeat the "Save" - "START" sequence as often as needed, until parameter changes are negligible. If you used only one set of frames for the initial refinement, or were keeping some parameters fixed, you may want to add more images or refine more parameters for later cycles. If refinement has converged to a reasonable looking set of parameters, that predict spot positions well, you are ready to proceed to integration.
"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 dps_refine or 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.
| Refine (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, click "Postchk" to bring up the Refinement Control window (or click "Refine" and then choose program "POSTCHK"). Turn on "Unit Cell", "Mosaicity", and "Xtal Orientation" in the "Refine:" list. Select the frames to use (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.
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 another refinement program, 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 profile fitting parameters, use the mosflm on-line help facility (type "help" at the MOSFLM => prompt in the Xmosflm window that you get by clicking "Index:MOSFLM") 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, the message window of the main GUI monitors the log file which is being generated (test_1_1_10_mosflm.log, e.g.). A sampling of images, with predictions, is displayed during integration. On the display, fulls are green, partials are yellow, overlaps are red, and reflections rejected by mosflm are magenta. Reasons for rejection include bad profile, too many background pixels rejected, and pixels greater than the overload value. When integration completes normally, the monitor window will show the "**** END OF PROCESSING ****" message from mosflm, followed by output file header information and a summary of the results:
.
.
.
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 scrolling back in the window or using an editor or xloggraph.
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 a browser such as netscape or 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 (CCP4) |
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(CCP4)" 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 V
This 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`
#
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 4
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 5
/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
coordinates from another file,
(4) construction of a control file and execution of the indexing program,
and (5) 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 $ref_limit"
Parameters for refinement of camera constants
The refinement parameters are the ones most likely to need changing. The
default values specify:
LIMITS EXCLUDE 10.0 25.0 40.0 50.0
where the two pairs of numbers specify the upper left and lower right corners of a rectangular area to be excluded from processing. The coordinates are in mm. and are relative to the scan origin. Multiple areas may be specified, up to a maximum of 10.
PROCESS 1 TO 3 ADD 0 START 0.0 ANGLE 1.0
becomes:
BEAM 111.3 100.5 PROCESS 1 TO 1 ADD 0 START 0.0 ANGLE 1.0 BEAM 110.3 102.3 PROCESS 2 TO 2 ADD 0 START 1.0 ANGLE 1.0 BEAM 112.2 101.6 PROCESS 3 TO 3 ADD 0 START 2.0 ANGLE 1.0
Mosflm command lines for "Integrate:Mosflm" that can be changed only by editing the command file "MosflmIntegrate.com" include all those listed above for refinement plus those created by the following lines:
set pr_0 = {"POSTREF SDFAC 3 SHIFTFAC 10.0 BEAM "}{$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_block
Most 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.
August 22, 2001