ADD
Increments batch numbers by a constant to every batch from this point on until another add command is read. Useful to make unique batch numbers from two or more files which have the same batch numbers inside. For example, Denzo_york1 format embeds the batch number in the .x file.
format ADD value
default nothing added
example ADD 1000 This will add 1000 to each batch number.
ADD PARTIALS
Tells the program to add partially recorded reflections among consecutive batches, even if the batches do not have consecutive numbering. Essentially obligatory.
modifier all partials are added over all consecutive batches
format ADD PARTIALS start1 to end1 start2 to end2 ... etc
default do not ADD PARTIALS
example ADD PARTIALS 0 to 49 51 to 99 100 to 149
Be sure that the ranges of numbers do not overlap.
ANOMALOUS
Flag for keeping Bijovets (I+ and I−) separate in the output file. If the ANOMALOUS flag is on, anomalous pairs are considered equivalent when calculating scale and B factors and when computing statistics, but are merged separately and output as I+ and I− for each reflection.
format ANOMALOUS
default not turned on (I+ and I− are combined)
example ANOMALOUS
B RESTRAIN
Can be used to restrain B factor differences from consecutive films or batches. The value which follows the flag represents the amount in 2 you will allow the B factors to differ from consecutive frames or batches. See also the keyword SCALE RESTRAIN.
format B RESTRAIN value_( 2) default not turned on
example B RESTRAIN 0.5
BACKGROUND CORRECTION
The BACKGROUND CORRECTION command specifies the amount per frame to increase background. Corrects for errors in SDMS (Hamlin) data integration in the software distributed in the late 1980s and early 1990s. The value given after the keyword increases the background by #counts/frame. Valid for archive file format only.
format BACKGROUND CORRECTION value_(#counts/frame)
default not turned on
example BACKGROUND CORRECTION 15
DEFAULT B FACTOR
Overall B used only in the absence of an INITIAL B FACTOR. You can apply a higher value to lower your Rmerge. Does not affect the quality of the data.
format DEFAULT B FACTOR value
default 0
example DEFAULT B FACTOR 5
DEFAULT SCALE
Overall scale factor used in the absence of an initial scale factor. This is useful if the data are too strong, which is sometimes the case with small molecules. It will reduce the output intensities by the factor entered.
format DEFAULT SCALE value
default 1
example DEFAULT SCALE 10
Useful to reduce the overall scale of the data set. If the numbers in the output file are too large, DEFAULT SCALE 10 will reduce them 10-fold.
DO NOT REJECT OUTLIERS
Turns off the reject outliers flag.
format DO NOT REJECT OUTLIERS
default DO NOT REJECT OUTLIERS
outliers not rejected automatically, but see REJECT OUTLIERS for more discussion.
ERROR SCALE FACTOR
This is a single multiplicative factor which is applied to the input σI. This should be adjusted, so the normal χ2 (goodness of fit) value that is printed in the final table of the output comes close to 1. By default, the input errors are used (ERROR SCALE FACTOR = 1). It applies to the data which are read after this keyword, so you can apply a different error scale factor to subsequent batches by repeating this input with different values.
format ERROR SCALE FACTOR value
default ERROR SCALE FACTOR 1
example ERROR SCALE FACTOR 1.3
good starting value for format denzo_ip
ESTIMATED ERROR
The estimate of the systematic error for each of the resolution shells. There must be exactly the same number of error estimates here as there are NUMBER OF ZONES. So if you have 10 zones, you need 10 numbers following the keyword estimated error - one for each zone.
The error estimates to do not all have to be the same. The estimated error applies to the data which are read after this keyword, so you can apply a different error scale factor to subsequent batches by repeating this input with different values. This is an important point if you enter data from a previous Scalepack output that does not need its σ to be increased.
The error estimates should be approximately equal to the R-factor in the table at the end of the output for resolution shells where statistical errors are small, namely the earlier resolution shells where the data is strong. This is a crude estimate of the systematic error, to be multiplied by I, and is usually invariant with resolution. Default = 0.06 (i.e. 6%) for all zones.
format ESTIMATED ERROR value1 value2 value3 value4 ...etc
default each value set to 0.06
example ESTIMATED ERROR 0.02 0.03 0.03 0.03 0.04 0.04 (6 zones)
EXTEND PARTIALS / DO NOT EXTEND PARTIALS
Some partially recorded reflections may be predicted by Denzo or Scalepack to start or end their Bragg condition in between consecutive frames due to small variations in crystal orientation from frame to frame. For these reflections only, there are two choices of defining where the reflection started (or ended): including the extra frame, or not. EXTEND PARTIALS tells Scalepack to include this extra frame. It only affects a very small fraction of the reflections. Opposite of DO NOT EXTEND PARTIALS.
format EXTEND PARTIALS
default this is the default
FILE
This specifies the files read by Scalepack. The input has two components. The first is a number. The second is a file name, which usually contains wildcard characters (###) that are incremented by the SECTOR command. The number which follows FILE specifies the starting batch number. A batch, previously called a film, can be as small as a single .x file (or the equivalent). It can be a group of .x files, even an entire data set. The most frequent content of a batch is a single .x file.
This conversion of files into batches is particularly useful if you want to scale more than one data set together. For example, let's say you want to scale 10 oscillation frames (numbered 1 through 10) from first data set with 37 oscillation frames (numbered 1 through 37) from another one. The FILE statement will take each of the individual .x files and assign them a batch number. Thus, you would enter something like this: FILE 1 'setone###.x' and FILE 101 'settwo###.x' (see Scenario 5d). Thus, batch numbers 1 - 10 will correspond to files setone001.x, setone002.x, etc. (assuming you used the SECTOR 1 to 10 command above FILE so that the wildcards would be substituted with numbers). The batch numbers 101 - 137 will correspond to files settwo001.x, settwo002.x, etc. the ### is replaced by the sector argument, not by the batch number.
format FILE value 'filename' (see also note below)
defaults None
example FILE 101 '/frames/scale/lysoz###.x'
The FILE must come after FORMAT because the syntax depends on which input format is being read. The FILE must not be followed by a number in the case of the archive, denzo_york, and denzo_york1 formats, where the number after the word FILE is not given because the batch numbers are already stored in the file. If you want to change the batch numbers in these file formats, see the ADD command described above.
FIT
Tells the program what parameters to fit in post-refinement and specifies the group of files over which the fitting is to be performed. Postrefinement fit can be applied to an entire set of batches (one batch being the entire set of frames, for example) using the modifier crystal, or to each individual input file using the modifier film or batch.
modifiers CRYSTAL specifies that the fit operation is over the entire set of frames specified by a range and restrains the fit parameter to have exactly the same value over this range.
BATCH specifies that the fit operation is performed on each member of the set of frames specified by a range.
FILM alias for batch
parameters a*, b*, c* unit cell lengths. Values returned are real space
alpha* unit cell angles. Values returned are real space.
beta*
gamma*
rotx crystal orientation parameters deduced in Denzo
roty
rotz
wavelength incident wavelength..
mosaicity mosaicity as defined in Denzo, in degrees
format fit modifier parameter1 filmnumber to filmnumber
default the default is that nothing is fit unless specified
examples FIT crystal roty 1 to 137
FIT crystal mosaicity 1 to 5 7 to 10 102 to 104 to 137
FIT batch rotx 1 to 137
Most mistakes in Scalepack can be attributed to errors in FIT commands because the program is very sensitive to mistakes in the batch numbers. If you input non-existent batch numbers or define overlapping ranges (e.g., 1 to 10 5 to 20), the program is likely to fail in a strange way. If you specify a range of numbers, the program will only use the batch numbers that exist within the range. For example, if your batch numbers go from 1 to 40 and 70 to 90, you can get away with saying, say, FIT batch (parameter) 1 to 90, which is the same as FIT batch (parameter) 1 to 40 70 to 90. For FIT crystal, these two inputs are not equivalent. In the case of FIT crystal (parameter) 1 to 90, one value will be fit for all batches. In the case of FIT crystal (parameter) 1 to 40 70 to 90, two values will be fit, one for each range. Note that different parameters may be fit over different ranges and either over batch or crystal. You can also mix batch and crystal for the same parameters.
Do not fit unit cell parameters restrained by space group symmetry. For example, if you have space group P3, you must not fit b*.
Do not FIT batch rotz because this parameter is very poorly defined by the intensities of observed partial reflections. This is another very common mistake.
Unless you know what you are doing, do not FIT crystal rotx roty rotz, because if the spindle is even slightly misaligned, the assumption that there is only one crystal orientation parameter for a large sweep of data will force incorrect restraints on the crystal orientation refinement.
About fitting rotations: Changes in rotations, like crystal rotx roty and rotz, are expressed as small rotations, call them ∆, about the laboratory frame of reference. These ∆: ∆x, ∆y, and ∆z, are used because to a first approximation, they commute with one another (commute means that the order in which they are applied is irrelevant). This, in turn, is because these ∆ are small, typically less than one degree. The crystal or cassette rotations, Rx, Ry, and Rz, on the other hand, do not commute with one another because their values tend to be large (much greater than one degree). So when you ask Scalepack postrefinement or Denzo to fit these rotations, what is actually happening is that the ∆ are being refined. After each refinement cycle, the ∆ are converted into changes in Rx, Ry, and Rz by a (complicated) algebraic relation. Those of you with sharp eyes will have noticed in Denzo that the shifts reported by the program when fitting the crystal rotations do not correspond to the changes in the rot values. This is because the shifts reported are the ∆, not the changes in rotx, roty, and rotz. The other reason for fitting ∆ rotations the way they are defined in Denzo is to make them have a more intuitive correlation with the other parameters. Otherwise, changes in crystal rotz would not correlate with cassette rotz. This is of more importance in Scalepack, where only rotx and roty, and not rotz, are refined.
About fitting unit cell parameters: In both Denzo and Scalepack, the unit cell is fitted in reciprocal space, not real space. This means that for a non-orthogonal space group, refining the value of a* may end up changing the values of b and c, even though b* and c* remain the same. The same is true for the angles: fitting α* may end up changing β and γ, even though β* and γ* remain the same. So what you may notice sometime if you are not careful is that when you ask the program to fit crystal a*, but not b*, c*, and the angles, then a will not be a constant. a* will be constant, but when converted back to a when the other unit cell parameters have not been changes, a will not. The moral: when fitting unit cells, fit all the relevant parameters.
FIT B
This flag tells the program to refine B factors of every batch from the very first cycles of refinement. This is in contrast to the default procedure, where the B factors are fit only after the convergence of the scaling. In the default procedure, if scaling does not converge in 20 (default) cycles of refinement, B factors will be not be fitted. The FIT B command can override this. Not to be confused with the postrefine FIT B* command described above. You cannot postrefine B (temperature) factors.
format FIT B
default this flag is turned off
example FIT B
FIX B
This flag tells the program not to fit B factors at all. Usually, it is combined with the input of the B factors you want to apply but do not wish to refine anymore, or it is used for frozen crystals where you do not expect significant decay.
format FIX B
default turned off; B factors are fit after the scale factor refinement converges.
example FIX B
FIXED WINDOW
For Hamlin archive files a fixed window of 3, 5, 7, or 9 frames or the original Hamlin determined window of frames may be used for summing a reflection. Valid for archive file format only.
format FIXED WINDOW value
default uses the Hamlin definition of the window
example FIXED WINDOW 7
FORMAT
This keyword specifies the format of the input hkl and intensity data. Input data can come from any of the nine types of files. This program requires this keyword to properly read the files.
modifiers DENZO_IP from frames processed with Denzo
DENZO_YORK1 output created with Denzo option york
SCALEPACK from Scalepack output file
RIGAKU RAXIS binary R-Axis software output
XDS PROFIT.HKL binary output from XDS output file
MADNES PROCOR INTOUT binary madness output
MADNES PROCOR ASCII ascii madness output
XENGEN URF binary output from xengen. Also have to supply the program with info about frame width, in degrees, using frame width keyword.
ARCHIVE binary output from Hamlin software
format FORMAT modifier
default denzo_ip
example FORMAT denzo_ip ∗ if you use one of the binary formats that the data must be scaled on the same type of computer that created the binary files due to incompatibilities in number representations between computers.
FRAME WIDTH
Only for URF files created by Xengen. Other formats do not need this specification because Scalepack can read this information off the file header. The oscillation range for each frame.
format FRAME WIDTH value
default there is no default, this input is required for this format
example FRAME WIDTH 0.2
HKL MATRIX
Matrix for re-indexing. This matrix is applied to the hkl's as they are read in (applies to data read in after this command):
h' = (1)*h + (2)*k + (3)*l
k' = (4)*h + (5)*k + (6)*l
l' = (7)*h + (8)*k + (9)*l
Input is in the order (1....9). HKL MATRIX works with postrefinement. The program will not accept a matrix which has a negative determinant
format HKL MATRIX value11 value12 value13
value21 value22 value23
value31 value32 value33
default the default is the unit matrix
example HKL MATRIX 0 1 0 1 0 0 0 0 -1
transforms hkl into k h -l,
has the effect of switching a and b.
-1 is to keep the determinant positive.
HKL SCALE
Divides each h, k, and l by the input values. Useful for reducing the unit cell volume, particularly after hkl matrix transformation. Rarely needed. Example, index data originally in C222 and want your data in, say, P3, you would apply HKL SCALE of 2 2 1, and HKL MATRIX of 1 1 0 1 -1 0 0 0 -1 so that the new indices would have values of h +k/2, h-k/2, and l.
format HKL SCALE value1 value2 value3
default 1 1 1
example HKL SCALE 2 2 1
HKL SHIFT
Used to make a quick test of misindexing. Adds the specified integer vector to each original h, k, and l. If you are successful in using this, congratulations, you now have to reprocess your data in Denzo with the correct indexing.
format HKL SHIFT integer integer integer
default 0 0 0
example HKL SHIFT 0 1 0 we'll assume you weren't too far off
IGNORE OVERLOADS
Opposite of INCLUDE OVERLOADS. This is not the default. Useful if you collect data at low and high exposures and is useful to ignore the saturated reflections at the high exposures. This macro applies to data read in after this command.
format IGNORE OVERLOADS
default This is NOT the default See Include Overloads
INCLUDE OVERLOADS
INCLUDE OVERLOADS is a flag for whether fitted profiles with some pixels missing (typically due to overload) should be included in the scaling. Affects only Denzo image plate output files (formats denzo_ip, denzo_york1). Note that for summed profiles this does not apply because only profile fitting can estimate the value of the overloaded pixels.
format INCLUDE OVERLOADS
default This is the default
INITIAL B FACTOR
Table of starting B factors, one per batch, beginning on the record after the title. After running the program once, the output table of B factors can be cut out and pasted in here, for example, when you have set the FIX B flag and are not refining B values anymore.
format INITIAL B FACTOR batch no. b value batch no. b value ...
default value of the default B factor, which is defaults to 0
example INITIAL B FACTOR 1 0.0 2 0.1 3 0.1 4 0.1 5 -0.2 ...etc
INITIAL SCALE
Table of starting scale factors, one per batch, beginning on the record after the title. After one run of the program, the output table of scale factors can be cut out and pasted in here. This table is not required. If it is not included in the control input, then the DEFAULT SCALE is used (this is 1 unless otherwise specified).
If the initial scale factor is set to zero, that frame is ignored in the scaling and refinement.
format batch no. scale value batch no. scale value ...
default value of the default scale factor, which is defaulted to 1
example INITIAL SCALE FACTOR 1 1.0 2 0.9 3 0.0 4 0.85 5 1.1 ...etc.
INPUT / @
Redirection. Tells the program to read the file which follows the keyword. Same as in Denzo.
format @filename
default no redirection
example @reject
MERGE
Flag that tells the program to merge (combine, average) reflections with the same unique index. This is the Scalepack default.
format MERGE
default This is the default and need not be specified
MOSAICITY
Allows you to input the value of the mosaicity of the data set. This is normally read from the header of the .x file.
format MOSAICITY value
default read from the header of the .x file
example MOSAICITY 0.5
NO ANOMALOUS
Opposite of the keyword ANOMALOUS. Causes I+ and I- to be merged. This is the default.
format NO ANOMALOUS
default This is the default
NO MERGE
Flag for the output of unmerged (reflections with the same unique hkl are not combined) data. Opposite of MERGE. This is a very handy for specialized work. This flag has subsidiary modifiers include partials, original index or as default include no partials
modifiers INCLUDE PARTIALS all observations, both fully and partially recorded, are included in the output. The output will consist of the unique hkl, batch number, asymmetric unit, I, σ, and fractionality of the reflection. There is no information about I+ and I-, although it may be possible to get this in subsequent versions of the program.
INCLUDE NO PARTIALS only fully recorded reflections and those fully recorded reflections created by the summation of partials are included in the output. Partials which cannot be summed to a fully recorded reflection are lost. The output will consist of the unique hkl, batch number, asymmetric unit, I, and σ. This is the default for NO MERGE. There is no information about I+ and I-.
ORIGINAL INDEX the output will also contain the original (not unique) hkl for each reflection. This is designed for MAD/local scaling work. The original index modifier only works with the default INCLUDE NO PARTIALS. The output will consist of the original hkl, unique hkl, batch number, a flag (0 = centric, 1 = I+, 2 = I-), another flag (0 = hkl reflecting above the spindle, 1 = hkl reflecting below the spindle), the asymmetric unit of the reflection, I (scaled, Lorentz and Polarization corrected), and the σ of I. The format is (6i4, i6, 2i2, i3, 2f8.1).
format NO MERGE modifier
example NO MERGE original index
This command is also useful if you just want to combine all of the information contained in multiple .x files into a single file. Simply read in all of the .x files, don't do any scale or B factor refinement, and output NO MERGE include partials.
NO PROFILE TEST
This is a flag which operates only on ARCHIVE format files. Tells Scalepack that reflections with weird profiles should not be rejected. Opposite of PROFILE TEST.
format NO PROFILE TEST
default This is not the default
NUMBER OF ITERATIONS
The number of cycles for refinement of scale and B-factors. The default value is 20 cycles. If it is set to 0, the program computes statistics, merges reflections with the same unique hkl, and writes the output file based on the initial scale and B factors. Normally you do not have to specify this unless you want to avoid scaling.
format NUMBER OF ITERATIONS integer
default 20 iterations
example NUMBER OF ITERATIONS 0
NUMBER OF ZONES
The number of resolution shells the data is divided into for the basis of calculating statistics. This input is required and must match the number of zones specified under the ESTIMATED ERROR keyword. Handy tip: it's nice to set up the NUMBER OF ZONES to equal the number of zones used by X-plor for the output of refinement statistics by shell, for when you get around to publishing your data and refinement statistics together in a paper.
format NUMBER OF ZONES integer
default This input is required
example NUMBER OF ZONES 10
ORIENTATION AXIS 1
Three integer vector which describes the orientation of the vertical axis of the crystal.
Equivalent to Denzo and Scalepack keywords VERTICAL AXIS. This information is usually not inputted by the user, but subsequent versions will read it from the header of the .x files. This command does not affect scaling or postrefinement. However, it does affect the values of the misorientation angles reported in the Scalepack log file.
format ORIENTATION AXIS 1 integer integer integer
default 1 0 0
example ORIENTATION AXIS 1 0 1 0
ORIENTATION AXIS 2
Same as ORIENTATION AXIS 1 except describes the spindle axis of the crystal. Equivalent to Denzo and Scalepack keywords SPINDLE AXIS. Otherwise the same as above.
format ORIENTATION AXIS 2 integer integer integer
default 0 0 1
example ORIENTATION AXIS 2 1 0 0
ORIGINAL WINDOW
Refers to the window size of ARCHIVE format files. Opposite of FIXED WINDOW.
OUTPUT ANOMALOUS
Alias for the keyword ANOMALOUS.
OUTPUT FILE
Name of file for output of scaled measurements. A new file will be created if none exists, but a pre-existing file will be overwritten. Maximum of 80 characters allowed in the file name. Depending on whether the ANOMALOUS flag is set, there are one or two sets of I and σ(I) per reflection. The output is h, k, l, I, σ(I) (NO ANOMALOUS flag) or h, k, l, I+, σ(I+), I-, σ(I-) (ANOMALOUS flag) in format (3I4, 4F8.1). If the NO MERGE flag has been set, unmerged data are output as h, k, l, asymmetric unit #, I, σ(I) in format (4I4, 2F8.1) and the ANOMALOUS flag has no effect. For NO MERGE original index the format is: original hkl, unique hkl, batch (film) number, a flag (0 = centric, 1 = I+, 2 = I-), another flag (0 = hkl reflecting above the spindle, 1 = hkl reflecting below the spindle), the asymmetric unit of the reflection, I (scaled, Lorentz and Polarization corrected), and the σ(I). The format is (6i4, i6, 2i2, i3, 2f8.1).
format OUTPUT FILE name use single quotes for safety
default you must specify the output file name
example OUTPUT FILE '/people/myname/LYSOZ.sca'
POLARIZATION
This command allows you to correct a mistaken polarization/monochromator value entered when you ran Denzo. It saves you from the chore of reprocessing all of your original images once you have learned of a mistake. This is mainly for synchrotron users who collect very high-resolution data.
format POLARIZATION Denzo value corrected value
default The polarization is read off the header of the .x file
example POLARIZATION Denzo 0.0 corrected 0.9
POSTREFINE
The number of cycles of postrefinement to be done. Works in conjunction with the FIT commands described above. If you set the number of postrefinement cycles to zero, then postrefinement will be skipped even if you have FIT commands in your control file.
format POSTREFINE integer
default Postrefinement is not done unless you specify it
example POSTREFINE 10
This flag tells the program to print the results of the specified calculation after every refinement cycle. Useful in the case where one scales non-isomorphous data and wants to make the outlier list short by using the statement PRINT total chi2 200 PRINT single chi2 100.
modifiers TOTAL CHI2 cutoff for printing poor reflections. Total χ2 for all measurements of a reflection. Default = 52
SINGLE CHI2 cutoff for printing poor reflections. χ2 for any single measurement of a reflection. Default = 3.52.
CORRELATION / NO CORRELATION prints correlation matrix.
Default: no correlation
SOLUTION / NON SOLUTION prints new scale and B factors.
Default: no solution
SHIFTS / NO SHIFTS prints changes to scale and B factors.
format PRINT modifier
defaults PRINT total chi2
PRINT single chi2
PRINT no correlation
PRINT no solution
PRINT no shifts
New scale and B factors will always be printed if the number of fitted parameters exceeds 300.
PROFILE TEST
PROFILE TEST is a flag that can be turned on and off as desired. This is the default. Bad profiles can be used to reject a DCREDUCE summed hkl. Valid for ARCHIVE file format only. Opposite of NO PROFILE TEST.
PROFILES FITTED
This flag tells Scalepack how the profiles were treated by the indexing program (e.g., Denzo). The two choices for profiles are fitted and summed. Valid for denzo_ip, Denzo_york1, and xengen urf formats. Most of the time, people fit profiles, so this is the default and need not be specified in the command file.
format PROFILES FITTED
default This is the default
PROFILES SUMMED
The opposite of PROFILES FITTED. This is not the default and must be specified if true.
RECSQ
Metric tensor description of the reciprocal space unit cell. Why would you ever use this when you can specify the real space constants?
format RECSQ value1 value2 . value6
default same as UNIT CELL
example RECSQ 0.0001 0 0 0.0004 0 0.0009
[to describe unit cell 100 50 33 90 90 90.]
REFERENCE BATCH
Specifies which batch or film or set of batches or films will be the reference for the scaling and B refinement. The scale and B factor for these are not refined. More than one film or batch may be used as the reference. This is important only for crystals which decay during data collection. If the crystal is frozen and does not decay, then the default may be used, which is to let the eigenvalue filter define the overall scale and B factor. With a large number of batches, reliance on the eigenvalue filter is a little bit dangerous, so you should consider using a reference batch number in those cases.
This keyword is entirely equivalent to the keywords REFERENCE BATCHES, REFERENCE FILM, AND REFERENCE FILMS. The others exist because some people have a grammatical hangup about using the singular to describe more than one object.
format REFERENCE BATCH integer integer integer ... etc.
default no reference batch. Eigenvalue filter defines the overall scale and B
example REFERENCE BATCH 1 3 4 5
REFERENCE BATCHES, FILM, FILMS
Same as reference batch
REJECT HKL
This flag tells the program to reject the list of individual h, k, l's which follow. This is useful for iterative rejection cycles since the file containing the rejected reflections can be reread. Each record after the title contains one reflection with the variables h, k, l (original index) and film number in free format. This information is most easily edited from the printed output of a previous run, can contain the whole line. One can read it from a reject file with command @reject.
format REJECT HKL
default This is not the default
REJECT OUTLIERS
Automatic rejection of outliers. Not yet reliably implemented. This is supposed to replace multiple rounds of running Scalepack. The idea is that when this keyword is set, Scalepack runs once, makes a reject.dat file, then runs again, reads the reject.dat file and scales the data based on the reduced set of observations.
REJECTION PROBABILITY
Applies Bayesian rejection of outliers. Rejected observations are written to the reject.dat file (see WRITE REJECTION FILE). The whole hkl (all original hkls with the same unique hkl) with at least one observation with a probability of being an outlier greater than or equal to the value specified after the WRITE REJECTION FILE keyword (default 0.9) are written to the log file. This is an estimation on your part of how frequently you expect any observation to be an outlier. In principle, the rejection probability should be about equal to the number of outliers divided by the number of observations. A good value to use is 1/10,000, i.e. 0.0001, for normal good data. If you have a non-random signal in your background (e.g., satellite crystals, malfunctioning detector, ice rings), then you will probably have to increase the rejection probability. If you do not want to generate a reject list in the log file, then omit the keyword. A comparison of R-linear and R-squared is often helpful for deciding whether to increase the rejection probability. See the discussion following Scenario 1 for more on this.
The rejection algorithm used in Scalepack is the most sensible and statistically sound outlier rejection algorithm. Unlike some other programs, the Scalepack outlier rejection is based on comparing differences to σ. So it will typically reject, say 4 or 5 σ outliers. Some reflections with a large discrepancy from the average value of I may simply represent a lack of adequate statistics in measurement and not a "mistake" (non-random error) in measurement. If a reflection has a large discrepancy from the average and a large σ, its contribution to the average will be very small anyway.
Here's an example of how the outlier rejection algorithm works:
|
Input data (after scaling) |
||
|
Obs # |
I |
σ |
|
1 |
10.0 |
0.1 |
|
2 |
10.1 |
0.1 |
|
3 |
9.9 |
0.1 |
|
4 |
11.0 |
0.1 |
|
5 |
20.0 |
10.0 |
Although you may think that {5} is the outlier, in fact the consistent set of observations will be {1, 2, 3, 5}, and {4} will be the outlier. Why is this? A consistent average will be 10.0 (or more exactly 10.000003), because observation 5 has a 1/1000000 lower statistical weight than the other observations, due to its large σ. Observation 4, on the other hand, which was measured more accurately, will be 8.7 σ deviations from the average of the remaining observations because the expected error of the difference 4 - <{1,2,3,5}> is 0.115, and 8.7 = (11.0 - 10.000003) / 0.115. So the observation with the largest deviation from the average is not necessarily a statistical outlier.
R-merge (after outlier rejection) will be very bad, 25%, even if the average is measured extremely well, with a sigma of 0.057%! This has to do with R-merge being an unweighted statistic, and I/σ being a weighted statistic. If some other program rejected observation 5 (for no good reason) and observation 4 (for good reason), R-merge would be 0.067%. Practice shows that most programs would reject observation 5 because many users want a good Rmerge. And sometimes these programs would not even flag the true outlier - observation 4!
format REJECTION PROBABILITY value
default 0.0001
example REJECTION PROBABILITY 0.0001
RESOLUTION
Minimum d-spacing for this run. Default is the maximum resolution found in the input data. One can supply two numbers in any order, and they will be minimum and maximum d-spacings.
format RESOLUTION value [value]
default highest resolution detected in .x file
examples RESOLUTION 10 2.2
RESOLUTION 2.2
RESOLUTION STEP
Changes the number of reflections per shell for the purposes of printing out statistics. Formally, it represents the exponent of the zone volume calculation. Normally, this is 3, because the volume of a sphere goes as radius cubed, so all the statistics shells will have the same number of reflections. Changing the resolution step could be useful to prepare a table of statistics to compare with other programs which may print out the statistics differently.
format RESOLUTION STEP value
default RESOLUTION STEP 3
example RESOLUTION STEP 2.5
SCALE ANOMALOUS
This is the flag for keeping Bijvoets (I+ and I-) separate both in scaling and in the output file. If the SCALE ANOMALOUS flag is on, anomalous pairs are considered non-equivalent when calculating scale and B factors and when computing statistics, and are merged separately and output as I+ and I- for each reflection.
This is a dangerous option because scaling may be unstable due to the reduced number of intersections between images. The danger is much larger in low symmetry space groups.
SCALE ANOMALOUS will always reduce R-merge, even in the absence of an anomalous signal, because of the reduced redundancy. However, χ2's will not be affected in the absence of an anomalous signal.
format SCALE ANOMALOUS
default This is not the default. Use with extreme caution.
SCALE RESTRAIN
Can be used to restrain scale factor differences from consecutive films or batches. The value which follows the flag represents the amount you will allow the scale factors to differ from consecutive films or batches. It adds a factor of (scale1 - scale2)2/(scale restrain)2 to the target function minimized in scaling. This only applies to batches between which you add partials. For very thin frames, this is almost obligatory. The value should roughly represent the expected relative change in scale factors between adjacent frames.
format SCALE RESTRAIN value
default not turned on
example SCALE RESTRAIN 0.01
(expect 1% change between adjacent frames)
SECTOR
Substitutes for the ### wildcard to specify a group of files to be read. See FILE keyword.
format SECTOR integer to integer
default no default
example SECTOR 1 to 40
SECTOR WIDTH
Sector width can be specified in degrees. A pseudofilm is a sector width's worth of data from one detector. Valid for area detector data only, default value 5 degrees.
format SECTOR WIDTH value
default 5 degrees
example SECTOR WIDTH 3.0
SIGMA CUTOFF
Cutoff for rejecting measurements on input. Default = -3.0. Be careful if you increase this!
What is the rationale for using σ cutoff -3.0 in Scalepack? Wouldn't you want to reject all negative intensities? Why shouldn't you use a σ cutoff 1.0 or zero? The answer is as follows: The best estimate of I may be negative, due to background subtraction and background fluctuation. Negative measurements typically represent random fluctuations in the detector's response to an X-ray signal. If a measurement is highly negative (≤ -3σ) than it may be more likely the result of a mistake, rather than just random fluctuation. If one eliminates negative fluctuations, but not the positive ones before averaging, the result will be highly biased. In Scalepack, SIGMA CUTOFF is applied before averaging. If one rejects all negative intensities before averaging a number of things would happen:
1. The averaged intensity would always be positive;
2. For totally random data with redundancy 8, in a shell where there was no signal, there would be on average 4 positive measurements, with average intensity one σ. This is because the negative measurements had been thrown out. So the average of the four remaining measurements would be about 2 σ! This would look like a resolution shell with a meaningful signal!
3. R-merge would always be less than the R-merge with negative measurements included
4. A SIGMA CUTOFF of 1 would improve R-merge even more, by excluding even more valid measurements!
Why should this worry you? Exclusion of valid measurements will deteriorate the final data set. One may notice an inverse relationship between R-merge and data quality as a function of SIGMA CUTOFF So much for using R-merge as any criterion of success.
Even the best (averaged) estimate of intensity may be negative. How to use negative I estimates in subsequent phasing and refinement steps? The author of Scalepack suggests the following:
1. You should never convert I into F
2. You should square Fcalc and compare it to I. Most, but not all of the crystallography programs do not do this. That is life. In the absence of the proper treatment, one can make approximations. One of them is provided by French and also by French and Wilson and implemented in the CCP4 program TRUNCATE. A very simplified and somewhat imprecise implementation of TRUNCATE is this: if I > σ(I), F=sqrt(I) if I < σ(I), F=sqrt(σ(I))
format SIGMA CUTOFF value
default -3
example SIGMA CUTOFF -2.5
SPACE GROUP
Space group symbol from the list below. This input is required! The space group may be entered as a name (e.g., P212121) or as a number (e.g., 19, for the same space group). Most of the numbers correspond to those of the International Tables. The numbers above 230 are nonstandard definitions of space groups.
|
1 |
P1 |
89 |
P422 |
154 |
P3221 |
207 |
P432 |
|
3 |
P2 |
90 |
P4212 |
155 |
R32 |
208 |
P4232 |
|
4 |
P21 |
91 |
P4122 |
168 |
P6 |
209 |
F432 |
|
5 |
C2 |
92 |
P41212 |
169 |
P61 |
210 |
F4132 |
|
16 |
P222 |
93 |
P4222 |
170 |
P65 |
211 |
I432 |
|
17 |
P2221 |
94 |
P42212 |
171 |
P62 |
212 |
P4332 |
|
18 |
P21212 |
95 |
P4322 |
172 |
P64 |
213 |
P4132 |
|
19 |
P212121 |
96 |
P43212 |
173 |
P63 |
214 |
I4132 |
|
20 |
C2221 |
97 |
I422 |
177 |
P622 |
303 |
P2C |
|
21 |
C222 |
98 |
I4122 |
178 |
P6122 |
305 |
B2 |
|
22 |
F222 |
143 |
P3 |
179 |
P6522 |
318 |
P21221 |
|
23 |
I222 |
144 |
P31 |
180 |
P6222 |
401 |
C1 |
|
24 |
I212121 |
145 |
P32 |
181 |
P6422 |
403 |
P21C |
|
75 |
P4 |
146 |
R3 |
182 |
P6322 |
446 |
H3 |
|
76 |
P41 |
149 |
P312 |
195 |
P23 |
455 |
H32 |
|
77 |
P42 |
150 |
P321 |
196 |
F23 |
501 |
I1 |
|
78 |
P43 |
151 |
P3112 |
197 |
I23 |
503 |
I2 |
|
79 |
I4 |
152 |
P3121 |
198 |
P213 |
505 |
C21 |
|
80 |
I41 |
153 |
P3212 |
199 |
I213 |
|
|
Notes to particular space groups:
|
|
146 R3 |
R3 in hexagonal setting |
|
446 H3 |
R3 in primitive setting |
|
|
155 R32 |
R32 in hexagonal setting |
|
|
455 H32 |
R32 in primitive setting |
|
|
401 C1 |
Non-standard, but useful to make angles close to 90. |
|
|
501 I1 |
Non-standard, but useful to make angles close to 90. |
|
|
303 P2C |
P2, C axis unique |
|
|
403 P21C |
P21, C axis unique |
|
|
305 B2 |
like C2, B face centered, c axis unique |
|
|
503 I2 |
Non-standard, but useful to make beta angle close to 90. |
|
|
SPINDLE AXIS |
|
|
Alias for ORIENTATION AXIS 2.
UNIT CELL
Real cell specified as a, b, c, alpha, beta, gamma. UNIT CELL is included in the header of Denzo_IP, Denzo_york1, ARCHIVE, and Scalepack files. Otherwise, it must be included.
format UNIT CELL value value value angle angle angle
default the value from the first header encountered
example UNIT CELL 50 62 100.3 90 90 90
The postrefined value of the unit cell constants is not used, nor is it output in the Scalepack
output file. You must get this information from the log file if you are interested in it.
VERTICAL AXIS
Same as ORIENTATION AXIS 1
WRITE BADDIES
Writes *.xrej files so that reflections from the reject file may be displayed by XdisplayF. Not fully implemented. Will terminate the program and prevent scaling and postrefinement.
Note that the command @reject must precede the input of the .x files.
WRITE REJECTION FILE
Creates a file with hkl's to be rejected. UNIX file name: reject, VMS file name:
REJECT.DAT. Reject file is created if it does not exist. If the file exists, it is overwritten.
You can specify the threshold for what you consider to be a rejectable probability. The default is 0.9, which is fairly safe, but you may want to decrease this to, say, 0.5 on later rounds of rejection.
format WRITE REJECTION FILE value
default Does not write the rejection file, but if it does, the default value is 0.9
example WRITE REJECTION FILE 0.5