STRAT

• Commands
• Examples
• References

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Commands

The following are the available commands. The commands marked with a star (*) are mandatary to the program, and those without star are optional.

ALIGN*, ANOMALOUS, CELL*, CHI0*, CONTINUE, CONVENTION, CYCLE, DETECTOR*, FORMULA, F-BEST, F-DONE, F-LEFTOVER, F-SCRATCH, INCLUDE, LIST, OMEGA0*, PHI0, RESOLUTION*, STRATEGY*, SYMMETRY*, WVL and !comments.

ALIGN alignment_1, alignment_2

ALIGN defines the standard or ideal alignment, e.g. A*//-X, B//Y. The corresponding angles, ( omega_a, chi_a, phi_a ), are called alignment angles. The matrix listed in the output of STRAT labeled as (astar/bstar/cstar) is the so called orientation matrix U [2] (ie. the transpose of the A matrix in Reference 1). The (omega_a, chi_a, phi_a) can be calculated from the so called rotation matrix F [2] (ie. the matrix inv. M(omega_a, chi_a, phi_a) in Reference 1). The values of the rotation matrix elements depend on the definition of (omega, chi, phi), which may be different from system to system. Comparing the alignment matrix in the STRAT output and that of the area detector software is always a good idea, to make sure the consistency of their conventions.

ANOMALOUS switches the anomalous option to on. In this case a Friedel pair is considered to be two independent reflections. There is no parameter for this card.

CELL inputs the cell parameters of the real crystal cell.

CHI0 inputs the alignment chi angle. The reciprocal lattice should be aligned as is specified with the ALIGN command, when the crystal is at (omega_a, chi_a, phi_a).

CONTINUE continues a strategy with one or more omega-sweeps, which may not be able to be included in one STRATEGY card.

This card defines the rotation angles relative to the x (vertical up), y (+z cross to +x), z (from x-ray source to the crystal) coordinate system. The three integer numbers will defines the rotation directions of phi, chi and omega (yes, here the order is phi, chi and omega) when all of them are at zero positions. The general conventions are

                 ccw~x:1, ccw~y:2, ccw~z:3
           and   cw~x:-1, cw~y:-2, cw~z:-3

where cw stands for clock wise and ccw stands for count clock wise. For example, the program default is that +phi is vertical down (-x or -1), +chi is horizontal from crystal to x-ray source (-z or -3), and +omega is vertical down (-x or -1). Therefore an explicit input would be

                 CONVENTION -1 -3 -1

CYCLE defines the number of calculation cycles to accumulate the best strategies, and the number of tries of this kind of accumulation. The default input is 0 and 1. In the default case, no best strategy will be selected. The output will be the data completeness of every input strategy. Although the total cpu time is proportional to the number of tries, it is not proportional to the number of cycles, because only the so called leftover reflections are used in the later cycles. An accumulation of the best strategies will automatically terminate if the gain of newly collected reflections is zero. It provides the user an option to let the program determine how many omega-sweeps are sufficient.

DETECTOR defines the detector parameters for the two squared area detectors. The parameters include crystal to detector distance the size of the detector and the 2theta angle. There should be one card per detector. They are distinguished by the detector ID (0 or 1, in case of Xuong-Hamlin system). These parameters will be used for the entire calculation. In other words, the area detectors are assumed to be fixed during a data collection. One important thing in choosing the detector parameters is to make sure the two detectors together will cover the resolution shell to be collected. Giving some freedom on the high resolution edge, e.g. 0.1 Å, sometimes may improve the efficiency. If case of one detector system, only one DETECTOR card is required.

FORMULA defines the condition of allowed reflections. The reflection condition may be copied from the International Table of Crystallography, e.g. -h+k+l=3n for a hexagonal cell of R32 space group. If the index of a reflection violates the formula, it will be excluded from the list of reflections to be tested. FORMULA card can be used to exclude reflections of systematic absence. Up to three FORMULA cards can be input. This card always causes a new version of scratch file to be created.

F-BEST defines a file to store the best strategy, if option CYCLE is used. Note that for the reason of the order of motor movement on a Xuong-Hamlin system, the order of the omega-sweeps accumulated in F-BEST file may not be proper to use directly. Sorting the selected omega-sweeps by chi angles usually can prevent collisions of the goniometer with other hardware parts.

F-DONE defines the file containing the previously collected reflections. These reflections and the symmetry related ones will be excluded from the list of reflections to be tested. The reflection file is in HKL/TNT format (3xHKL,1x,3I4). The indices of these input reflections will be used to calculate the indices of pseudo reflections to be excluded. In case that there is a body systematic absence, the cell_shrinking_ratio should be either set to 1.0 plus a FORMULA card, or set to a small number (e.g. 0.3) to make sure that the result of interpellation will not miss any pseudo reflections.

F-LEFTOVER defines the leftover file, which has the same format as the scratch file , but contains the reflections left by the last tested strategy. This file can be used as the input scratch file for the next circle of calculations.

F-SCRATCH defines the scratch file which contains the initial reflections. If the file exists and is consistent with the other input parameters, the initial reflections will be read from it. Otherwise STRAT will create a new one.

INCLUDE defines an input parameter file, which may contain any of the input cards, including INCLUDE card itself. For example, the symmetry operators and/or the STRATEGY cards can be input from separate files for convenience.

LIST defines the number of independent reflections to be list out. LIST card is useful for checking the symmetry operators, since the symmetry related reflections should be of the same resolution.

OMEGA0 inputs the alignment omega angle.

PHI0 inputs the alignment phi angle. The default is 0.0.

RESOLUTION defines high and low resolution limits.

STRATEGY starts to define a new strategy. A STRATEGY card contains the starting and ending omega angles for an omega-sweep (omega_0 and omega_1), the starting chi angle (chi_0), chi angle increment (delta_chi) and number of increment in chi (#chi), as well as starting phi (phi0), phi angle increment (delta_phi) and number of increment in phi (#phi). For a one-omega-sweep strategy, both #chi and #phi should be set to 1. The total cpu time is roughly proportional the number of STRATEGY cards. STRATEGY cards can be easily created by a user written program for user's special purposes, where the consideration of avoiding physical collision of moving mechanical parts is helpful to determine a practically useful strategy.

SYMMETRY defines the symmetry operator(s). International table format is expected. There should be one SYMMETRY card for each symmetry operator. Only is the rotation part of the symmetry operator used in STRAT. Therefore, for none primary lattice space group, only the symmetry operators which are directly related to the origin are needed. Input of the redundant symmetry operators will not affect the result of a calculation, but it will increase the number of total sample reflections, therefore slow down the calculation. In the current version, up to 32 symmetry operators can be input.

WVL defines the wave length and the cell_shrinking_ratio. The default are 1.54 and 1.0, respectively. If the cell_shrinking_ratio is set larger than 100, it will be interpreted as a proposed number of sampled reflections, and will be used to determine a cell_shrinking_ratio. Otherwise, it must be equal to or less than 1.0, and the lattice constants will be multiplied by this value.

Any input line starting with a semicolon ; or an exclamation mark ! will be ignored as comments.

Examples

 $! This is an example command file of STRAT 
 $! for T4 Lysozyme P3221. A 10x15° sweep
 $! strategy is chosen from about 1000 
 $! one-sweep sweeps. The cell dimensions 
 $! are shrunk so that the number of sample
 $! reflections is about 4000.
 $! The data completeness is about 90%.
 $
 $ create strat.inp
 ; T4 lysozyme wild type enzyme, cell parameters
 Cell      61.2 61.2 96.8 90. 90. 120. 
 ; read in symmetry operators of space group P3221 
 SYmmetry  x,y,z
 SYmmetry  -y,x-y,z+2/3
 SYmmetry  y-x,-x,z+1/3
 SYmmetry  y,x,-z
 SYmmetry  -x,y-x,-z+2/3
 SYmmetry  x-y,-y,-z+1/3
 ; set resolution limit to 2. and 20.Å
 Resolution      2.0 20.
 ; align the crystal so that the a* axis parallel to Y and c* parallel to -X
 Align     A*//Y,  C*//-X
 ; input alignment omega_a chi_a phi_a angles
 Omega0    -58.12 
 CHi0      -89.36
 Phi0      26.63
 ; detector 0: distance=615.mm, size=300.mm, 2theta=-34°
 ; detector 1: distance=569.mm, size=300.mm, 2theta=18°
 Detector  0 615.4 300. -34.
 Detector  1 568.7 300. 18. 
 $
 $ run strat_exe:strat.exe
 ; input the parameter file strat.inp
 Include   strat.inp
 ; input strategy file containing 880 single-omega-sweeps.
 Include   880_sweeps.dat
 ; set the pseudo reflection number to 4000 
 Wvl       1.54 4000
 ; create a file which contains the output best strategy 
 F-Best    best.dat
 ; define a scratch file 
 F-Scr     scr1.bin
 ; One strategy of 10 omega-sweeps is wanted
 CYcle     10  1
 $ 
 $! Confirm the best-strategy by using the real cell parameters
 $ run strat_exe:strat.exe
 ; the same parameter file as the above
 Include   strat.inp
 ; Input the best strategy calculated from the previous run
 Include   best.dat
 ; Now the real cell parameters are used. 
 Wvl       1.54 1.
 ; Another scratch file will be created, to keep the first one for another search.
 F-Scr     scr2.bin
 $ exit

 Strategy  -30.   -15.,   -90. 0.0  1,    0.0 0.0 1
 Strategy  -25.   -10.,   -90. 0.0  1,    0.0 0.0 1
 Strategy  -20.    -5.,   -90. 0.0  1,    0.0 0.0 1
 ....

 sweep  Omega   Omega     Chi    Phi   %more  %total
       #start     end            
     1     0.0   15.0    65.0   135.0   25.6    25.6
     2    10.0   25.0   -15.0    45.0   20.1    45.7
     3   -30.0  -15.0   -40.0   135.0   13.2    58.9
     4    -5.0   10.0    15.0    45.0   13.5    72.4
     5   -15.0    0.0   -50.0   135.0    7.0    79.4
     6   -10.0    5.0    10.0   135.0    6.5    85.9
     7   -20.0   -5.0    10.0    45.0    3.4    89.3
     8    10.0   25.0   -15.0   135.0    2.9    92.3
     9   -15.0    0.0   -85.0    90.0    2.1    94.3
    10    15.0   30.0     0.0    45.0    2.9    97.2

References

2. International tables of x-ray crystallography, vol. IV, section 3, Angle settings for four-circle diffractometers.