cad hklin1 foo_in_1.mtz hklin2 foo_in_2.mtz
... hklini foo_in_i.mtz hklout foo.mtz
[Keyworded input]
Uses:
The input files are one or more (up to 9) reflection data files in MTZ format, assigned to HKLIN1, HKLIN2, ... HKLIN9.
The output file is a reflection data file in MTZ format.
Missing data items, i.e. empty column entries corresponding to reflections that occur in some input files but not in the input file contributing that particular column, are represented by Missing Number Flags (see VALM keyword). A particularly important example of this is the use of CAD to fill in missing data in a dataset with MNFs, thus completing the dataset. More details can be found in the unique documentation.
The various data control lines are identified by keywords, those available being:
CELL, CENTRIC ONLY, CTYPIN, END, HISTORY, LABIN(compulsory), LABOUT, MONITOR, OUTLIM, REFMONITOR, RESOLUTION, SCALE, SORT, SYMMETRY, SYSAB KEEP, TITLE, VALM
In addition, there are a few keywords for editing dataset information in the MTZ file header:
DCELL, DNAME, DRENAME, DPNAME, DWAVELENGTH, XNAME
(Compulsory.) A line giving the names of the input data items to be selected from FILE_NUMBER <i> to be read from HKLIN<i>. Up to 29 columns can be specified for input from each HKLIN<i>. If you want to pick up all items from a file, AND there are less than 30 items excluding H K L, then you can specify
e.g.: LABI FILE_NUMBER 1 E1=F E2=SIGF E3=FC E4=PHIC ... E29=SIGFau (E<j> stands for ENTRY<j>.)
A line giving the new names for the data items which will be written to HKLOUT. Output labels can be changed if you wish, but the default is to keep the input label, unique-ified with the input file number if necessary (see above). E.g.:
This changes the first 2 labels and leaves all the rest the same.
A line giving the names of the data types to be assigned to the entries selected for FILE <i> . The default is to leave the input datatypes unaltered.
The data types for the different types of data which can be present
in an MTZ file are as follows;
H F J D G K Q L M P W A B Y I R [ U V ]
It is essential to have correct column types for PHASES and ANOMALOUS differences:
In addition two special data types are used to signal that you are preparing data for translation functions of various types. They are:
There must be only one FCpart PHICpart per input file, and they must be the last items specified for LABIN. CAD generates equivalent reflections using only the ROTATIONAL part of the primitive symmetry operator; (i.e., if the spacegroup is P212121 these reflections are analysed as though the spacegroup was P222) This is allowed for in the TFFC and RSEARCH programs. See their documentation.
For the above example their output labels would be
FC1 PHIC1 FC2 PHIC2 ... FCnsymp PHICnsymp
where nsymp is the number of primitive symmetry operators.
See example.
This keyword is now obsolete, since it is no longer appropriate to use one set of cell dimensions to cover all datasets held in the file. The keyword will be ignored! Please see DCELL keyword.
Only output centric terms.
History strings to be added to mtz o/p file HKLOUT
Printing MTZ file header information as:
- NONE
- (default) no header information output
- BRIEF
- brief header output
- HIST
- brief + mtz history
- FULL
- full header output
Defines limits for the OUTPUT file. Use this for expanding data to cover more of reciprocal space. Subsidiary keywords:
- SPACEGROUP <name or number of spacegroup>
- this is used to choose a Laue code defined for the appropriate point group. The name (or number) corresponds to the spacegroup whose limits are used. NB : This does NOT alter the symmetry operators stored in the mtz file. In the unlikely event of wanting to change these, use the key word SYMM.
- HKLLIM <hmin> <hmax> <kmin> <kmax> <lmin> <lmax>
- used to set your own choice of hkl limits. It is better to use the spacegroup to choose a Laue group. Using HKLLIM often duplicates reflections with a zero index.
Spacegroup Laue code limits are: PG1 h k l : l >= 0 Spacegroups 1,2 h k 0 : h >= 0 0 k 0 : k >= 0 P2/m h k l : h >= 0, l >= 0 h k 0 : h >= 0 Spacegroups 3,..(bsetting) Pmmm h k l : h >= 0, k >= 0, l >= 0 Spacegroups 16,.. P4/m h k l : h >= 0, k >= 0, l >= 0 0 k l : k > 0 0 0 l : l > 0 Spacegroups 75,.. P4/mmm h k l : h >= 0, k >= 0, l >= 0, h >= k 0 0 l : l > 0 Spacegroups 89,.. P3 (R3) h k l : h >= 0, k > 0 0 0 l : l > 0 Spacegroups 143,.. P312 h k l : h >= 0, k >= 0, k <= h (all l) h 0 l : l >= 0 Spacegroups 149,151,153,.. P321 h k l : h >= 0, k >= 0, k <= h (all l) h h l : l >= 0 Spacegroups 150,152,154,.. P6/m h k l : h >= 0, k >= 0, l >= 0 0 k l : k > 0 0 0 l : l > 0 Spacegroups 168,.. P6/mmm h k l : h >= 0, k >= 0, l >= 0, h >= k 0 0 l : l > 0 Spacegroups 177,.. P23 h k l : h >= 0, k >= 0, l >= 0, l>=h, and h k h : k >= h h k l : k > h if l > h Spacegroups 195,.. P432 h k l : h >= 0, k >= 0, l >= 0, k >= l and l>= h Spacegroups 209,..
The program prints lots of information about every <nmon>-th reflection (default 0).
Use either:
<dmax>, <dmin> are the resolution limits for the data to
be included, i.e. data are included for which
(1/<dmax>)**2 >= 4 sin**2theta/lambda**2 >=(1/<dmin>)**2
NOTE: Defaults are 0.1 and 1000.0 Angstrom.
Specifies <scale> (and optionally <temperature_factor>) to be applied to all items in FILE_NUMBER which are flagged as type F D Q (or G L for F+ F- alternatives), i.e. all items except intensities and PHASES.
(If no <temperature_factor> is supplied then the <scale> only is applied.)
If there is one number for <temperature_factor>, that is taken as an ISOTROPIC correction, and the scale is applied as <scale> exp( -<temperature_factor>s**2)
If there are six numbers B11 B22 B33 B12 B13 B23 for <temperature_factor>, that is taken as an ANISOTROPIC correction and the applied scale is:
<scale> exp{- [ B11*h*h*(a*)(a*) + B22*k*k*(b*)(b*) + B33*l*l*(c*)(c*) + 2.0*(B12*h*k*(a*)*(b*) + B13*h*l*(a*)*(c*) + B23*k*l*(b*)*(c*) ] }
Example:
scale file_number 1 1 4.722 4.722 -7.08 2.36 0 0
would apply the anisotropic correction to file 1 according to the formula above with a unit scale factor (i.e. <scale> = 1) and temperature factor parameters:
| B11 | = | 4.722 |
| B22 | = | 4.722 |
| B33 | = | -7.08 |
| B12 | = | 2.36 |
| B13 | = | 0 |
| B23 | = | 0 |
Sort order for indices H K and L, e.g.
SORT H K L SORT L K H
This means that the first index will be the slowest, the second the intermediate, and the last the fastest varying, e.g. SORT H K L will have H slowest, L intermediate and K fastest. Note that SORT H K L is the default sort order (i.e. that used in the absence of the SORT keyword), so that SORT is only necessary when you require a sort order which is different from this default.
This can be used to change the symmetry operators in the output file. The default is to keep the symmetry of the first input file, HKLIN1.
Keep systematic absences in output file. (The default is to reject them.)
Title to be used in output log file and in output hkl file.
The Missing Number Flag (MNF) written to HKLOUT is set to <valml>, which can take the value NaN or be a real number. If this keyword is not set, then the value of the MNF is taken from the header of HKLIN1 or set to NaN if it is not present there. If NOOUTPUT is specified then reflections with all data items missing are not output to HKLOUT.
Terminate input.
For information on the underlying data model, and its representation in MTZ files, see the MTZ format document. For information on the use of datasets in Data Harvesting, see the Harvesting document.
The XNAME and DNAME keywords are for assigning columns to existing or new datasets. The keywords DRENAME, DPNAME, DCELL and DWAVELENGTH are for changing details of existing datasets. It may be possible to mix several keywords in a program run, but the more complicated combinations will probably give weird results. A sequence of well-defined program runs is probably safest.
N.B. The old PNAME keyword is now obsolete. The project name is now considered an attribute of the crystal. It has an administrative role for Data Harvesting, but is not part of the data structure. Columns are therefore assigned according to XNAME/DNAME only.
XNAME FILE_NUMBER 1 E5=toxd XNAME FILE_NUMBER 2 E2 TO E4=toxd XNAME FILE_NUMBER 3 E1=toxd E2 TO E4=rnase E5 TO E6=toxd XNAME FILE_NUMBER 4 ALL=toxdThis keyword can be used to assign a crystal name where there was previously none, or to replace an existing assignment.
A dataset, as listed in the MTZ header, is specified by a crystal-name/dataset-name pair. The crystal-name specifies a particular physical crystal, while the dataset-name specifies a particular dataset contributing to the structure solution. If either the XNAME keyword or the DNAME keyword or both are specified for a particular column, then the dataset assigned for that column will be changed (either to an existing dataset, or a new one). There should only be one XNAME card per file (use continuation lines if necessary).
A dataset, as listed in the MTZ header, is specified by a crystal-name/dataset-name pair. The crystal-name specifies a particular physical crystal, while the dataset-name specifies a particular dataset contributing to the structure solution. If either the XNAME keyword or the DNAME keyword or both are specified for a particular column, then the dataset assigned for that column will be changed (either to an existing dataset, or a new one). There should only be one DNAME card per file (use continuation lines if necessary).
The printer output first gives details taken from the input control data.
Then, for each input reflection data file, the information in the MTZ header, according to the requested level of monitoring. The labels are checked for consistency with those in the file, and the list of output labels is prepared.
The reflection data for each file is read and a summary table of the data is output .
The total number of reflection records in the output file is printed, followed by a summary of HKLOUT.
mtzutils, rsearch, tffc, unique.
Eleanor Dodson, York University