SCSB X-Ray Crystallography Center

SMART Quick Users Guide


SMART

Contents

For additional help using any of the software pakages please see the SOFTWARE help section of this center's HOMEPAGE.

SMART {Top}

SMART is a DOS based program which must be run from DOS and not a DOS window or shell. Navigating the SMART MENU
{enter} or LEFT MOUSE BUTTON = ACCEPT, GO-perform data collection, pick.
{esc} or RIGHT MOUSE BUTTON = CANCEL, QUIT, go back.
{ctrl-break} = STOP immediately and return to user control.

A TYPICAL Data Collection

  1. Setting Up
  2. Measure X-beam and Y-beam
  3. Crystal Alignment
  4. Orientation Matix run(s)
  5. Indexing
  6. ASTRO: obtain optimum data collection parameters (optional).
  7. Data collection run(s).
  8. SAINT: Data processing
  9. XPREP: Data merging

Setting Up { Top }

For SMART to function properly it must have the correct configuration parameters set up

CONFIGURE / EDIT

These are the parameters you may need to change:

Frame directory: m:\myo\ -This must point to an existing directory, including \
X-ray Source wavelength: 1.54184 -for Cu Ka
Direct beam X: 506 -These can be measured by an attenuated direct beam shot
Direct beam Y: 500 -These values change with D, and after filament changes
Create Large frames: Y -This produces 1024x1024 frames, which is recommeded


 

Measuring X-beam and Y-beam {Top}

The beam position must be measured whenever the detector distance is changed.  This cannot easily be done with a sample mounted on the goniometer since the beam-stop needs to be removed.

  1.  Place the 0.2 mm Ni filter in the Gobel optics assembly
  2.  Remove the beam stop
  3. set all goniometer angles to zero:           GONIOMETER / DRIVE / 0 0 0 0
  4. take a 2-10 sec. exposure:                      ADD
  5. measure the beam centroid:                    CURSORS / BOX
  6. Replace the BEAMSTOP and remove the 0.2mm Ni FILTER
Now enter these values in the SMART CONFIGURE menu

Crystal Alignment {Top}

Crystal alignment is performed in MANUAL mode, using the x40 optical microscope and the manual control box.

GONIOMETER / OPTICAL

THE MANUAL CONTROL BOX HAS THE FOLLOWING FUNCTIONS

  • To align the goniometer head X axis || to your viewing plane:

    •  

    +X = PHI / AXIS PRINT
    -X = CHI / AXIS PRINT

  • To align the goniometer head Y axis || to your viewing plane:

    •  

    +Y = TTH / AXIS PRINT
    -Y = OMG / AXIS PRINT

     THE MICROSCOPE MOUNT IS NOT SOLID. Therefore do not expect the crosshairs to be aligned. Use the half-the-difference method to find the correct center.

    The Half-the-Difference-method

    First center on the crosshairs. Then with the crystal postioned at "+X" note the position on the right edge of the crystal. Then rotate to "-X" and move the right edge so that is half way between the "+X" and "-X" positions. Repeat the proceedure for "Y". Repeat for both "X" and "Y" until method converges.

    Orientation Matrix {Top}

    The orientation matrix is required to properly align the sample for complete data. There are two ways to get the orientation matrix. The first method is optimisd for small molecule (Mo) data collections, the second is recommended for Macromolecules (Cu). For quick screening a third method is very useful, but this does not produce an OM which is needed for optimizing data collection.

    The correct values must be entered into the program before collecting any frames.

    CONFIGURE / EDIT ( Distance, Xcntr, Ycntr, Image SIze)

    The exposure time should always match the dark current time. If it does not then a new DARK-CURRENT file should be either loaded (form an existing file) or created.

    1) The default method is recommended when using Mo radiation only. 3 scans are performmed two at + 10 deg and one at -10 deg. 2-theta.

    SCAN / MATRIX

    2) The standard method of obtaining an orientation matrix is to use a multi-run data collection.

    SCAN / EDITRUNS

    RUN Frame 2theta ....Omg .. Phi ... Chi .. Axis . Width .. #Frames .. Time(s) .. {seq}
    0 ....... 001 .....20.00 .... 0.00 .. 00.00 .. 0.0 .... 2 ......-0.15 ...... 15 ............ 30 ...... { 1 }
    1 ....... 001 .....20.00 .... 0.00 .. 90.00 .. 0.0 .... 2 ......-0.15 ...... 15 ............ 30 ...... { 2 }

    SCAN / MULTIRUN

    Name: MATRIX
    Title: Staphylococcal Nuclease
    max intensity: -1
    Suppress : N
    Suppress : N
    Suppress : N
    Oscillate: N

    The runs begin when you press {enter} or hit the LEFT MOUSE BUTTON

    3) Quick Lattice parameters - for when you are in a hurry.

    ADD

    Max seconds: 120 -this is a typical exposure time, increase upto 300 for small xtals
    Suppress correlation(Y/N): n
    Max Display Counts: -1
    Reset interval: 0.0
    Open & Close shutter (Y/N): y
    Disable dark/flood cor. (Y/N): n

    SAVE

    Output filename: pg_xtal.000

    SPATIAL / UNWARP

    Input frame filename: pg_xtal.000
    Output frame filename: pg_xtal.unw

    On the SGI now use the CCD2sol utility to reformat the unwarped pg_xtal.unw frame and create the DENZO com file.  This will auto-index the frame and provide you with cell dimentions, and a crude OM matrix.  Also the first frame of the normal SMART OM scan runs can be used in DENZO after unwarping.

    {ESC} - will STOP the data collection t the end of the current frame.
    {CTRL-BREAK} - will Terminate it immediately.

    After the data is collected a reflection list must be created and used for autoindexing:

    INDEXING {TOP}

    There are three ways to index your frames. The first method is the recommended one.  All frames used for indexing must be at the same detector distance, with the same Xcntr and Ycntr. The correct values must be entered in the SMART configure menu before data collection!

    1) This is the recommended method of indexing macromolecules using SMART. The other choices are
    2) SMART automated indexing,
    3) DENZO indexing.

    REFL_ARRAY / LOAD

    *.p4p -The correct data collection values must be enetered in the program, either by loading the appropriate P4P file or editing the CONFIGURE file.

    REFL_ARRAY / CLEAR

    Clears the reflection list, making it ready for addition of your data.

    REFL_ARRAY / THESHOLD

    Note: When working on the remote (UNIX) machine be sure to enter the correct D, X-cntr and Y-cntr values using either: CONFIGURE / EDIT or REFL-ARRAY / LOAD

    First input frame name: MATRIX0.001
    # frames to process: 15
    Max pixel seperation: 1
    Raw count threshold: -1 -This may need to be >1000 for non-frozen disorded samples
    I/Sigma threshold: 10   -use 5 for weak data
    Minimum excludedX: 908  -this should exclude the beam stop & LP region
    Maximum excluded X: 1024 -Measure X values using CURSORS/PIXEL
    Radius cutoff: 600
    Minimum Angstroms: 1.5
    Maximum Angstroms: 30
    Temperature Factor: 10

    REFL_ARRAY / INDEX

    Expected A-axis length: 48 -Known cell is needed as a seed, or
    Expected B-axis length: 48 -Measure cell using CURSORS/VECTOR
    Expected C-axis length: 63
    Expected alpha cell angle: 90
    Expected beta cell angle: 90
    Expected gamma cell angle: 90
    Axis length deviation: 0.3 -0.05 if cell is known
    Cell angle deviation: 0.1 -0.03 if cell is known
    Assume known Cell: N -Do not use, it does not work
    Verbose Output: Y
    Minimum # Vectors: 5 -reduce for poor or weak data, increase for good data (range:1 - 20)
    Length fraction for group: 0.30
    Fractional HKL deviation: 0.20 -Increase if indexing has trouble (max 0.4)
    Fraction which must be fit: 0.80 -decrease for poor or weak, 0.4 for twinned xtals

    Indexing problems are most frequently caused by using incorrect detector parameters.

    REFL_ARRAY / BRAVAIS

    Lattice Type: P -You must use P (primative) lattice here
    Max Sigmas for any soln: 25
    Max sigmas for best soln: 10

    Pick the lattice type for your crystal.  Sometimes this routine will choose the wrong bravais lattice, check the output for the correct choice and enter it at the prompt.

    REFL_ARRAY / LEASTSQ

    Lsqrs/Constraint type : 6 -Choices: 0=P(linear only), 1=P, 2= Mono-C, 3=Mono-B, 4=Mono-A, 5=Ortho, 6=Tetr, 7=Hex, 8=Rhomb, 9=Cubic
    Lsqrs/Constraint type : -6 -Negative numbers are used for subsequent refinement, so that refined offsets are used. A problem crystal may need an initial value of 1
    Max Allowed RLV dev: 0.01
    Frame Halfwidth: 0.05 -divide the frame width in degress by 2
    Constraint Mask: 768 -Use 771 for long axes, or if beam center wanders (recommended)
    Output Parameter file: MATRIX1._pr

    After obtaining the OM you should display it as an overlay to the frame being displayed.

    DISPLAY / HKL OVERLAYS

    -OR-

    2) This is the SMART automated threshold/bravais/index/Lstqrs routine. It will work well if the Xbeam Ybeam centers are good and the crystal is strongly diffracting. Since it chooses the bravis group automatically, it is likely to choose the wrong one! Try method 1 or 3 if this fails.

    REFL_ARRAY / AUTO

    RUN #1: MATRIX0.001
    RUN #2: MATRIX1.001
    RUN #3: $NULL
    RUN #4: $NULL
    #FRAMES: 15
    BRASS PLATE: $NULL
    LOWER AXIS: 30 {< lowest of a b c }
    UPPER AXIS: 100 {> highest of a b c }
    HKL TOLERANCE: 0.1
    LS TOLERANCE: 0.01
    MIN VETORS: 3

    After obtaining the OM you can display it as an overlay to the frame being displayed.

    DISPLAY / HKL OVERLAYS

    -OR-

    3) DENZO autoindexing of SMART images. NOTE: This requires only one image!

    The SMART 2k image can be converted into a format readable by DENZO using the command:

    CCD2sol {filename(s)}

    Which automatically produces a denzo.com file: dz_filename.com.  Use SPACIAL / UNWARP on the frame first to apply the spacial correction to your image ( Note the UNIX version of UNWARP does not work). The frame can then be indexed by using XdisplayF to do a {PEAK SEARCH}

    sol {filename}

    and then run the denzo com file. If you need to convert a large number of CCD images to DENZO readble format use:

    CCDconvert {filenames}

    To look at old DENZO files or the save your *.com files use:

    dz-list or dz-save

    to display the most recent denzo.com files.

    The DENZO OM convention is different from that used in the SMART-ASTRO-SAINT software suite. Use the following script to generate a Bruker *.p4p file from the denzo *.x file.

    DZ2P4P {filename} - Not ready yet

    To create a large oscilation or long exposure image, use the following utillity to add together a series of frames into one frame:

    CCDadd {filenames} - Note frames are NOT unwarped!

    Data Collection {Top}

    Data Collection begins with the choice of image size, detector distance and exposure time.
    A simple data collection is performed in a single pass, with the detector offset. The choice of offset angle and detector distance will be determined by the diffraction resolution and d-spacing. The exposure time MUST match that of the current DARK CURRENT frame.

    SCAN / SingleRun

    #frames: 900
    2-theta: 20.0
    Omg: 20.0
    Chi: 54.74
    Scan Axis: 2          -2=Omega scan, 3=phi-scan (do not use phi for data collection)
    WIDTH: -0.10           -xtal will hit detector if this is positive
    Seconds: 30           -this must match the exposure time of the current DARKCURRENT frame
    TITLE: Staphylococcal Nuclease Y27W crystal 123
    NAME: SNSY27W    -{max 7 characters, 8th char. is run#}
    RUN#: 0
    START FRAME#: 001
    MAX DISPLAY: -1
    Suppress (Y/N): N
    Suppress (Y/N): N
    Suppress (Y/N): N
    OSCILLATE (Y/N): N

    Do not touch the keyboard or mouse durring a data collection or it may be ABORTED.

    {ESC} - will STOP the data collection t the end of the current frame.
    {CTRL-BREAK} - will Terminate it immediately.

    Advanced Data Collection {Top}

    With the PLATFORM system there are many different options available to the user which are not posible with a single-axis fixed detector system. The multi-run option permits automatic variation of several data collection parameters during a data collection. The user may: ASTRO is a data collection strategy program which is used to suggest optimal data collection parameters, which are then used in the MULTIRUN menu.

    APPENDIX

    DARK Current {Top}

    The exposure time should always match the dark current time. If it does not then a new DARK-CURRENT file should be either loaded from an existing file or created.

    DETECTOR / LOAD DARK

    If a dark current file of the correct exposure does not exist you will need to creat one.  THIS IS RECOMMENDED whenever starting a new data collection.

    DETECTOR / NEW DARK

    EXPOSURE TIME: 60
    # AVERAGE: 15
    MAX DISPLAY: -1
    OUTPUT: MMYY_SSS._DK {please use this format-offenders will be severely rebuked and scorned}

    Detector Distance {Top}

    The detector distance is adjusted manualy and the value, in cm, entered into the smart software.

    CONFIGURE / EDIT / DISTANCE [enter D] / WRITE

    The detector distance combined with the 2-Theta angle will determine the resolution edge and maximum resolved d-spacing. Use this table as a rough guide. Remember it is always better to move the detector back and fill the detector with your data than it is to move it too close.
     

    edge (A) Det.(cm) TTH (deg.) max-AXIS (A) pos(omg-2tth) max-2TTH (deg.) maxR(A)
    1.25 5.0 38.0 90 11.0 110 0.86
    1.39 6.0  33.5
    1.54 7.0  30.0
    1.69 8.0  27.0
    1.85 9.0  25.0
    2.00  10.0  23.0  ???  ???  130  0.794
    2.16  11.0  21.0
    2.32 12.0  19.5
    2.49 13.0  18.0
    2.65  14.0  17.0  230+  55.0  ???  ???
    2.81 15.0  16.0
    2.98 16.0  15.0
    3.14 17.0  14.5
    3.31 18.0  13.5
    3.48 19.0  13.0
    3.65 20.0  12.5

    Frame Size {Top}

    The 2k CCD offers a choice of two frame sizes: The size of the image is determined by the configuration file smart._cf, which you can edit:.

    CONFIGURE / EDIT [create large frames (Y/N)] / WRITE

    The choice of frame size will determine which FLOODFIELD and SPACIAL correction files will be needed.

    DETECTOR / LOAD FLOOD
    LOW => C:\FRAMES\I800L140._FL
    HIGH => C:\FRAMES\I800H140._FL

    SPACIAL / LOAD
    LOW => C:\FRAMES\I800L140._IX or C:\FRAMES\I800L075._IX
    HIGH => C:\FRAMES\I800H140._IX or C:\FRAMES\I800H075._IX

    ASTRO {Top}

    ASTRO is a program for choosing optimal data collection parameters.

    >astro

    After starting ASTRO the first step is to load in your OM determined using SMART's autoindexing.

    The OM does not include the SPACE GROUP, so this must be entered manually Now you are ready to optimise your experimental runs To calculate the %completeness for this run This is an iterative process to maximize your %completeness. Go back and edit the data collection parameters, increase or decrease phi in steps of 20 deg., or change the omg start angle. DRIVE your view to those angles set in the data run. Try SCANing phi to find the best orientaion to put most of the unique volume into the detector, and omg to start with the unique volume just about to touch the ewald sphere.
     

    SAINT { Top }

    SAINT is a program for integrating frames, sorting refelection lists, scaling, filtering, sorting and merging of reflections. Although saint can be used to merge reflections it is recommended that XPRED is used to merge the symmetry related reflections after scaling and filtering the reflection list in SAINT. Several refinement contraints can only be entered on the command line:

    saint [/k1:lattice_type] [/l1:constraint_mask] [/bg:bgnd_scale] [/ls:lst_squrs_profile] [/t:int_box] [/h:memory]

    XPREP { Top }

    Xprep is a small utility for merging of symmetry related reflections in a list. It is used after SAINT has integrated, scaled, and filtered the reflection list.

    DOS {Top}

    The following DOS commands may be usefull.

    copy {filenames} {path\filename}...........COPY
    move {filenames} {path\filename}...........MOVE
    dir {optional path}........................LIST files
    cd {path}..................................Change Directory
    cd {..}....................................Back up directory tree
    c {enter} ................................ cd to the C:\ HD
    m {enter} ................................ cd to the m:\ HD
    pwd .......................................Print Working Directory
    mkdir {dirname}............................Make a New Directory
    type {filenames}...........................Print file to screen
    edit {filename}............................GUI file editor

    Note: The DOS format change directory commands:
    m:
    n:
    o:
    will also work on the SGI workstation to get you to these same directories. These call specific unix utilities and are not applicable to any other directories.
    { m: => /data4/bruker2k/, n: => /data5/, o: => /data6/ }

    Page created by Mark A. White on or about February 1998

     

    © 1998 - Page last maintained 6/98
    Copyright © 1998 The University of Texas Medical Branch