STRATEGY
usage: STRATEGY subkeywords
subkeywords: AUTO ROTATE SEGMENTS SIZES START END PARTS SPEEDUP ANOMALOUS NOTANOM ALTERNATE
The STRATEGY option allows the design of a data collection strategy in a semi-automatic way for a single axis rotation camera. Normally it is run from the imosflm GUI after indexing.
If run from from keyword input in ipmosflm, it requires all the parameters normally used to process a set of images (crystal symmetry, orientation, crystal to detector distance, wavelength, detector type, direct beam position). The type of detector MUST be set using a DETECTOR keyword.
Use keyword EXIT or END to end the strategy option.
AUTO
usage: Determine the starting phi angle and the phi rotation
required to give a complete dataset (if possible from a single crystal setting), and give statistics on completeness and multiplicity. Do NOT use START or END with the AUTO keyword.
If no START keyword is given, then AUTO mode will be the default, so if you give a ROTATE keyword there is no need to give an AUTO keyword
ROTATE
usage: ROTATE <phirot>
Only for use with the AUTO option. Restrict the total rotation to "phirot" degrees, rather than the full rotation for this Laue group and crystal setting. If no AUTO keyword has been given, ROTATE must be given before a SEGMENT keyowrd.
SEGMENTS
usage: SEGMENTS <nseg >
Only for use with the AUTO option. Allow "nseg" discontinuous segments of data to give a total rotation of PHIROT degrees. Unless specified explicitly with the SIZES keyword (see below) the segments will have approximately equal widths in phi.
Default: If in AUTO mode and no SEGMENT keyword is given, then one segment will be assumed. eg ROTATE 60 is equivalent to AUTO ROTATE 60 SEGMENT 1
SIZES
usage: SIZES <size1,size2,size3...>
The sizes for the "nseg" segments. If SIZES are given, then the "phirot" value given on the ROTATE keyword is ignored, and the total rotation is the sum of the SIZES.
Default: Use approximately equal sizes with total "phirot"
START/END
usage: START <phistart>
END <phiend> As an alternative to AUTO mode, specify the start and end phi values to be used in generating the reflection list. Up to 10 different sets of START and END can be given on successive STRATEGY keywords. eg STRATEGY START 0 END 30 STRATEGY START 35 END 60 STRATEGY START 70 END 90
PARTS
usage: PARTS <nparts>
If data have already been collected from other crystals, or some data has already been collected from the current crystal, set "nparts" to the total number of crystals (including the current crystal whose phi range is to be determined). See example below. This need only be given on the first STRATEGY keyword.
SPEEDUP
usage: SPEEDUP <factor>
The calculation can be speeded up by reducing the cell size. This can be particularly useful for large cells (eg greater than 100A) although inevitably there will be some loss of accuracy. However, providing there are a few thousand reflections generated the loss in accuracy is small. Suitable values for "factor " are 5-20.
Default: The program will automatically calculate a suitable SPEEDUP factor based on the unit cell size if no value is specified.
ANOMALOUS
usage: ANOMALOUS
Including this keyword will optimise the completeness of anomalous pairs rather than unique data. To cancel optimisation of anomalous data, use keyword NOTANOM
NOTANOM
usage: NOTANOM
Use this to cancel optimisation of anomalous pairs rather than completeness of unique data.
ALTERNATE
usage: ALTERNATE
When working with an orthorhombic spacegroup, the algorithm used to determine the best starting PHI value when using the AUTO mode is successful in approximately 90-95% of cases, but in some cases it fails. As a result, the best predicted completeness may be 3-4% less than it should be. To check this, a separate STRATEGY run should be performed including the keyword ALTERNATE. This chooses an alternative starting phi value and may, rarely, give a higher predicted completeness.
This is only necessary for orthorhombic space groups.
The rotation range (PHITOT) required to collect a complete dataset is determined from the crystal symmetry and orientation (eg 180 degrees for Laue group P2/m if rotating about the b axis, 90 degrees if rotating about a or c).
The phi value (PHIZONE) which places the unique symmetry axis in the plane normal to the X-ray beam and containing the rotation axis is determined, and a reflection list corresponding to a total rotation of PHITOT starting at phi=PHIZONE is generated.
This reflection list is then compared to a list of all unique reflections for this spacegroup and the completeness and multiplicity is calculated, both as a function of rotation and resolution.
It is assumed that all possible reflections are measured (ie none are lost because of spatial overlaps or because they extend over too many images). However, some reflections may be unobserved because they lie in the cusp region. The percentage of reflections within the cusp will depend on the wavelength, crystal symmetry and crystal orientation, and can be minimised by trying to orient the crystal so that the crystal axis closest to the rotation axis is at least THETAMAX degrees AWAY from the rotation axis, where THETAMAX is the maximum Bragg angle.
It is often possible to collect data with a very high percentage completeness with a total rotation significantly less than PHITOT. This will inevitably result in a lowering of the overall multiplicity, but if data collection time is limited (for example at a synchrotron source) it is preferable to obtain a dataset with high completeness and less than optimal multiplicity rather than an incompete dataset with higher multiplicity !
If the total rotation angle to be collected is specified, and the number (up to 3) of discontinuous segments to be used, the program will determine the start and end phi values for each segment that will give the highest possible completeness. For example, a total rotation of 60 degrees in 2 segments for an orthorhombic spacegroup will result in the identification of two 30 degree segments which give the highest completeness.
If some data has already been collected from one (or more) previous crystals, the program will determine the starting phi value for the "current" crystal that will give the maximum completeness, with the assumption that the phi rotation for this crystal is such that the TOTAL rotation for ALL the crystals is PHITOT (This assumes that all crystals are mounted about the same axis). The user may also define the rotation angle for the current crystal.
Trying other phi ranges
After the initial calculation of completeness, the program will give the prompt:
STRATEGY ==>
Typing STATS at this prompt will give full statistics on completeness and multiplicity as a function of rotation angle and resolution.
The effect of using other total rotations and different numbers of segments can also be tested (but using more than 3 segments is very time consuming)
eg (AUTO) ROTATE 40 SEGMENTS 2 RUN
will find the best two segments of 20 degrees each for maximum completeness (the AUTO keyword can be omitted).
Alternatively, the completeness of specified segments can be tested:
START 0 END 20 START 65 END 90 RUN
Note that the phi ranges specified on the START and END keywords MUST lie within the phi range generated by the program when it first starts. Thus if, for example, the keywords STRATEGY AUTO ROTATE 60 were specified, then it is not possible to try: AUTO ROTATE 90 SEGMENTS 1 RUN at the STRATEGY prompt (The program will complain).
Use keyword EXIT or END to end the strategy option.
Examples
usage: Example command files
(i) This example is to determine the best starting phi and phi rotation to collect data from an orthorhombic crystal, whose orientation is defined by the UMATRIX and MISSET keywords. More usually a MATRIX file will be supplied, as written by REFIX.
STRATEGY SPEEDUP 20 DISTANCE 80 DETECTOR MAR UMATRIX 1 0 0 0 1 0 0 0 1 CELL 50 50 80 90 90 90 MISSET 12.0 13.4 15.0 SYMM 19 BEAM 90 90 DIVERGENCE 0.35 0.3 MOSAIC 0.2 SEPARATION 1.5 1.5 HKLOUT strategy.mtz POLARISATION MONOCHROMATOR WAVELENGTH 1.5418 RUN(ii) Example of the case when data have already been collected from one crystal
See the User Guide for further examples.
In this case data have been collected from phi = -20 to 19 from one crystal with missetting angles 12.0,13.4,15.0. A second crystal is mounted, which has missets of 7 23 -40. This run will determine the best phi range for this second crystal to complete the data. Normally the first crystal will have been collected starting at a zone. If this is NOT the case, it will probably be necessary to collect two segments of data from the second crystal to get complete data. This can be done by specifying "STRATEGY AUTO SEGMENTS 2" for the second crystal, and it may be advantageous to specify the sizes of the two segments. Thus if the first crystal was collected starting at 15 degrees away from a zone, for a total of 35 degrees, then the second crystal will need one segment of 15 degrees and another of 40 degrees (90-35-15) to get best completeness.
STRATEGY start -20 end 19 PARTS 2 DISTANCE 80 DETECTOR SMALLMAR UMATRIX 1 0 0 0 1 0 0 0 1 CELL 50 40 73 90 90 90 MISSET 12.0 13.4 15.0 SYMM 19 BEAM 90 90 DIVERGENCE 0.35 0.3 MOSAIC 0.2 SEPARATION 1.5 1.5 HKLOUT strategy.mtz POLARISATION MONOCHROMATOR WAVELENGTH 1.5418 GO STRATEGY AUTO MISSET 7 23 -40 GO