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CCP4i: Graphical User Interface |
| Reflection Data Utilities Module |
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The layout of each task window, i.e. the number of folders present, and whether these folders are open or closed by default, depends on the choices made in the Protocol folder of the task (see Introduction). Although certain folders are closed by default, there are specific reasons why you should or may want to look at them. These reasons are described in the Task Window Layout sections below.
This is an interface to the SFALL program which generates Fcalc and PHIcalc from either input coordinates or a map. You must give the name of an input coordinate or map file and also an MTZ file into which the calculated Fs and PHIs are added. You will need to identify the FP and SIGFP in the MTZ file. If a FreeR column is also identified, the FreeR set of reflections will be excluded from the calculation. By default the calculated Fs and PHIs will cover the same resolution range as the one already in the MTZ file.
The Task Window for the SFALL Task is relatively simple. The Protocol folder has the choice between generating structure factors from coordinates or a map (after which the Files folder is adapted accordingly), and the option to scale the input Fp to the Fcalc.
After the Protocol and Files folders, the 'Cell Parameters' folder has the option of adapting resolution range, space group and/or cell parameters. The then following 'Program Parameters' folder allows the adaptation of Maximum atom radius used to build atom/residue mask and the amount to add to atomic Bfactors.
See program documentation: SFALL.
Standard CCP4 programs deal with reflection files in so-called MTZ format. Files in different formats, namely ascii MTZ ('na4'), X-PLOR/CNS, MULTAN, SHELX, TNT and user defined ascii, may be converted to MTZ format. Additionally, MTZ files may be extended to create a full unique set of reflections with various options to deal with freeRflags. The default setting is to create this set. At the start of a structure determination, it is advisable to always create this full unique set of reflections, which contains (h, k, l, F, SIGF, (I, SIGI), ..., FreeR_flag) for all observed reflections to the resolution limit available, plus entries for any unobserved reflection, all with freeRflags assigned. This never does any harm, and it is much harder to do satisfactorily at a later stage. For more information about a full unique set with freeRs, see also FreerUnique.
TRUNCATE, part of the Import Task when SHELX or MULTAN data is imported, is needed to convert intensities to structure factors. This is a genuine call for data harvesting, which is why the first folder beneath the Protocol and Files folders is concerned with 'Data Harvesting'. The user has the choice whether to allow data harvesting or not, but it is, of course, recommended. Input sensible (and/or appropriate, if the have already been assigned) project and dataset names.
See Data Harvesting in CCP4i for implications for the Interface.
F2MTZ is one of the data preparation programs that can handle data harvesting keywords PNAME and DNAME. See Data Harvesting in CCP4i for implications for the Interface.
To make things easier in the long run, it would be wise to think this through at this stage, and choose sensible project and dataset names. Input these in the 'MTZ Project & Dataset Names' folder directly beneath the Files folder.
Features to look out for in the Convert to MTZ & Standardise Task are:
| Protocol option | Folder title | Importance | Comment |
|---|---|---|---|
| all | Creating full/unique dataset | freeR | see FreerUnique |
| systematic absences | chance to include them in MTZ file | ||
| extend resolution | use artificially high resolution if more data is anticipated | ||
| all (not MTZ) | Detailed specification of import file format | Fortran format, data type and labels | see below |
| SHELX and MULTAN | Convert Is to Fs | run Truncate | see TRUNCATE program documentation |
| Data Harvesting and Convert Is to Fs | role of TRUNCATE in Data Harvesting | see above | |
| Convert Is to Fs | TRUNCATE protocol to be followed | Conversion to structure factors either by truncation according to French&Wilson, or by simply taking the square root of the intensities. See TRUNCATE | |
| user defined | Detailed specification of import file format | Essential for the successful running of the Task with this option. See also below |
The full "import" (i.e. Convert to MTZ & Standardise) task contains the following steps:
Pay special attention to the folder Detailed specification of import file format:
(5X,3F5.0,6X,2F10.0,7X,F10.0,/,10X,2F10.0,8X,F10.0,6X,F10.0)This complicated statement describes the following reflection file format:
INDE 6 0 0 FOBS= 1259.884 0.000 SIGMA= 38.561
FPART= 0.000 0.000 WEIGHT= 1.000 TEST= 0
The CCP4 Suite of programs is released with a set of example files. MTZ files are distributed in 'na4' format, which is a type of ASCII. In order to convert these to the MTZ format needed to run the programs, the program NA4toMTZ is provided. In the Interface, this is included within the 'F2MTZ' part of the 'Convert to MTZ & Standardise' task.
When browsing for an 'na4' file, do not forget to change the file extension to '.na4'.
These data types are not usually present, but are legal:
In addition, the program F2MTZ accepts the column type X for freeRflags originating from X-PLOR/CNS, and will reset the column type to I in the resulting MTZ file (see FreerUnique).
N.B. The column types of structure amplitudes and phases may not be any other than F and P, respectively. It is also essential to have correct column types for phases and anomalous differences, to distinguish:
See program documentation: F2MTZ, NA4toMTZ, UNIQUE, FREERFLAG, CAD, MTZUTILS, MTZLIB
MTZ files may be converted to several other formats, i.e. X-PLOR/CNS, MULTAN/RANTAN, SHELX, TNT, SCALEPACK, USER and CIF. Use this utility to output CIF-information, which is the default Protocol option.
CIF files can contain multiple datasets (from multiple MTZ files), but there is no provision for the output of derivative data in the same data block as native data. Therefore, each dataset needs to be put in a different data block. However, the Interface (or rather the CCP4 program performing the transformation) only caters for one MTZ file and thus one data block. Each CIF data block must have a name which should begin with the characters 'data_'. The Interface will derive a name from the input MTZ filename, but you can change it. You can not have unlimited numbers of columns; the MTZ program labels are restricted to:
| CIF label | MTZ program label |
|---|---|
| _refln.F_meas | FP (or F+ [and F-]) |
| _refln.F_meas_sigma | SIGFP (or SIGF+ [and SIGF-]) |
| _refln.F_calc | FC |
| _refln.phase_calc | PHIC |
| _refln.fom | FOM |
| _refln.intensity_meas | I+ [and I-] |
| _refln.intensity_sigma | SIGI+ [and SIGI-] |
Features to look out for in the Convert from MTZ Task are:
| Protocol option | Folder title | Importance | Comment |
|---|---|---|---|
| CIF | CIF Format Details | one data block per dataset | See Notes on CIF in the MTZ2VARIOUS Program Documentation |
| CIF, SHELX and XPLOR/CNS | MTZ File Labels | anomalous data | Friedel pairs are output as separate reflections if the anomalous difference is assigned. See also OUTPUT anomalous data in MTZ2VARIOUS Program Documentation |
| SCALEPACK | MTZ File Labels | I(+) and I(-) | pseudo-SCALEPACK output useable as input to the SOLVE package |
| USER | User Defined Output Format | See OUTPUT options and Notes on INPUT and OUTPUT in the MTZ2VARIOUS Program Documentation | |
| all | Infrequently Used Options | output modifications | get output in desired form |
See program documentation: MTZ2VARIOUS, MTZDUMP,MTZDMP, MTZTONA4,NA4TOMTZ, MTZUTILS
For more information on mmCIF, see The mmCIF Home Page at the IUCr.
Analyse, manipulate and convert structure factor files.
Features to look out for in the Edit MTZ File Task are:
| Protocol option | Folder title | Importance | Comment |
|---|---|---|---|
| set or change header information | default option | ||
| Change column labels and types | Change column label to | chance to make column label names that mean something to you | |
| reduce to asymmetric unit | choose CCP4, BIOMOL, TNT or user-defined | ||
| expand to lower symmetry | specify spacegroup to expand into, and choose asymmetric unit as before. Can also be done with CAD | ||
| sort reflections | sorting criteria | sorting on index can also be done with CAD, see below | |
| reindex reflections | transformation matrix | complicated transformations with translations are better dealt with by redoing the data reduction | |
| merge reflections | use only when you know why you have multiple reflections with identical indices | ||
| delete reflections | |||
| delete columns | |||
| generate Hendrickson-Lattman coeffs | |||
See program documentation: SFTOOLS, MTZUTILS, REINDEX, CAD
This task interfaces to the CAD program which can be used to:
To input more than one MTZ file, click on the Add input MTZ file button. By default all the data in the input MTZ file is put into the output file but you can change the Input option from 'all columns' to 'selected columns' and then select the columns using the Add column button. If you want to have the majority of the columns in the file, then click on the List All Columns button and then delete the columns you do not require using the Delete selected item option under the Edit list menu button. You will then need to select the column by clicking on one of the fields for that column with the right mouse button. See also Extending Frames and Toggle Frames.
CAD can not deal with more than 29 columns.
Do not include columns H, K and L in input. These are transferred to output automatically, and only upset the program.
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.
Features to look out for in the CAD Task are:
| Folder title | Importance | Comment |
|---|---|---|
| Define MTZ Output | override space group, cell dimensions, sort order, hkl limits etc. | can also be done with SFTOOLS, see above |
See program documentation: CAD, SFTOOLS
The columns of an MTZ file are divided between a number of datasets, which are each identified by a Project name (PNAME) and a Dataset name (DNAME). See the description of Data Harvesting for background information. The program CAD can be used to change the attributes of a dataset, and to change the assignment of columns to datasets, and this functionality is accessible through the Edit MTZ Project & Dataset Names interface.
The top half of the interface lists the current datasets and their attributes. Any attribute can be edited, and datasets may be added or deleted. The lower half provides a pull-down menu for each column allowing the user to select a dataset from the current list. Note that the input to CAD is taken from the list of columns, so that surplus datasets are ignored, and datasets deleted from the dataset list but retained in the column list are kept.
In principle, dataset information should be generated and propagated automatically, so this interface should only be needed to fix problems.
See Data Harvesting in CCP4i for implications for the Interface.
See program documentation: CAD
This is the option to use for reindexing 'standard' MTZ files, i.e. non-multi-record MTZ.
See program documentation: REINDEX
This is an interface to the data analysis tools of SFTOOLS which will perform several forms of analysis of Structure Factor data. The user should select an MTZ file and the data columns to analyse. The results are displayed automatically by The Loggraph Utility. The results are also saved in a .log file which can subsequently be viewed with the View Log Graphs option in the View Files from Job menu on the right hand side of the Main Window of CCP4i.
See program documentation: SFTOOLS
See program documentation: SIGMAA
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