SFTOOLS (CCP4: Supported Program)

NAME

sftools - Reflection data file utility program including some density map handling

SYNOPSIS

DESCRIPTION

The SFTOOLS program is a toolbox of commands to analyze, manipulate, and convert structure factor files. The program has been written with an interactive user in mind and will provide on-line help, suggestions and warnings as appropriate. A list of the currently implemented commands plus descriptions of their use is given in the command reference section at the end of this document. The list of commands can always be obtained by just pressing the return key when the program asks for a command. To get the command descriptions, the user should type the name of a command followed by the keyword HELP.

SFTOOLS is very flexible which gives the user great power to accomplish many tasks. At the same time the program contains many checks to protect you, as far as possible, from using the flexibility inappropriately. This design goal makes it more difficult to write a script to run the program as a batch job. If you have to make a script then you may find it easier to run the program once interactively and paste the commands into the script file as you go. At this moment it is not possible to obtain a log file of your interactive session, you will have to run the program from a script if you really need one. Creating a log file will be implemented in the next release of the program.

SFTOOLS has also some density map functionality. It can read/write, CCP4, BIOMOL and DSN6 maps, and it can create maps from structure factors and vice versa. A very useful combination is to create your map (FFT), cut out a block of density surrounding your protein (MAPLIMIT), and write it out as a DSN6 file (MAPOUT), all in one interactive session.

A lot of the functionality of SFTOOLS is also covered by a large number of other CCP4 programs. The main advantage of using SFTOOLS is that you can do all your manipulations and analyses in one session without having to run multiple programs and create script files and output files with intermediate results. In addition, many users like the interactive and user friendly nature of the program.

The rest of this manual consists of 3 parts:

General program description
Summary and examples of major commands
Command reference section

General program description

SFTOOLS consists of a central data base and a set of subroutines that interact with it. The data base consists of 3 large arrays plus several other variables to store the header information. When reading file formats with less information than the MTZ format the user is asked to supply the missing information.
Here are the four most important data base components:

IHKL: This is a 1-dimensional array that stores the reflection indices. Each index triplet is packed into a 4-byte integer which is used as a unique reflection identifier. Each index ideally occurs only once and obeys the CCP4 asymmetric unit definitions. Only multi-record MTZ files can have multiple reflections with the same indices. Unlike other CCP4 programs, indices are not considered as data base columns and their content can only be changed with the REINDEX command.
The size of the IHKL array is determined by parameter MAXREF in the sftools.inc file.
REF: The REF array contains all the actual data columns. In the program it is a 1-dimensional array, but it appears as a 2-dimensional array to the user, e.g. rows=reflections and columns=Fobs, Sigma, Phase etc... The user can identify a specific column by typing "COLUMN column_id". column_id is either the column label or the column number. The column label is case insensitive but may need to be quoted if it contains unusual characters. Labels will fail if columns with identical labels exist (bad practice). Column numbers should always work. Note that the indices do not count as columns so if your file contains H K L Fobs Sigma, then Fobs is column 1.
SFTOOLS can also read, write, and create density maps. Maps are stored at the end of the REF array whereas reflections are stored at the beginning.
The size of the REF array is determined by parameter MAXDAT in the sftools.inc file. The number of columns times the number of reflections in your file should be less then MAXDAT. At the same time the number of reflections should be less then MAXREF and the number of columns less then MAXCOL.
ACTIVE: The ACTIVE column is a boolean flag that indicates which reflections should be used and which should be ignored. Initially all reflections are "active" but this can be changed with the SELECT keyword. For instance to restrict all following commands to 10 - 3 Angstrom resolution you would type "SELECT resol > 3 < 10". You can use SELECT ALL to make all reflections active again.
The size of the ACTIVE array is determined by parameter MAXREF in the sftools.inc file.
TYPE: The TYPE array stores the column type of each column as a 1 character code. The codes follow the MTZ definition for column types. SFTOOLS actively uses the column types to prevent you from comparing apples and oranges, keeping phase information consistent etc.

Filling the data base

After starting the program you will want to load data into the data base. In most cases this means reading a structure factor file. To do this use the READ command. If the data base was empty then SFTOOLS will read both the header and the diffraction data. If a non-MTZ file is read the program will prompt for missing header information. If you read in a second structure factor file (or you prepared the header information with the SET ALL command or by reading a density map) then SFTOOLS will compare the header information on the second file with what is in the data base. It will report inconsistencies, but in all cases the information in the data base will be kept. It is useful to have an empty MTZ with header information for your project but no data. When reading a non-MTZ file then you first read the empty MTZ to get the header information. This way you avoid to have to enter the header information and the possible typos that that might introduce.

When a second (or more) structure factor file is read, the program will add new columns to the data base to store the data from the new file. Data for reflections that are already present in the data base will be appended to that reflection. Data for reflections that are not yet present in the data base will be stored in newly created reflections. In this case MNFs are inserted in the old columns (see the 0 0 1 reflection below). When a reflection was present in the data base but not in the new structure factor file, then the columns for the new structure factor file are set to MNF (see the 0 0 3 reflection below). An example is given below.

Assume that you have the following two structure factor files

file1.mtz              file2.mtz

0 0 2 12.4  3.2        0 0 1 82.7 10.1
0 0 3 68.7 12.1        0 0 2 13.8  3.8
0 1 3  3.2 17.0        0 1 3  4.8 17.2
0 1 5 34.0  5.8        0 1 5 37.1  4.8

in SFTOOLS you type:

read file1.mtz
read file2.mtz

The data base will then contain

0 0 1  MNF  MNF 82.7 10.1
0 0 2 12.4  3.2 13.8  3.8
0 0 3 68.7 12.1  MNF  MNF
0 1 3  3.2 17.0  4.8 17.2
0 1 5 34.0  5.8 37.1  4.8

SFTOOLS will merge, sort and check your data. For further consistency checks you can give the CHECKHKL command after reading a file. This also gives you a few seconds to think about your next action while CHECKHKL is working.

Data representation

All data, including integers, are stored as real numbers. Phase information is stored in radians but they will appear in degrees to the user (as long as the column type is set to "P"). RFREE flags follow the CCP4 definition in which the data is divided into N RFREE sets with flags running from 0 to N-1. When reading/writing non-MTZ files, the RFREE flag definitions will be converted to/from the CCP4 definition, respectively. The RFREE set with a flag of 0 is considered to be the actual RFREE set.

When reflections have missing data in one or more of their columns, then this is indicated by a Missing Number Flag (MNF). SFTOOLS uses a value of -1.0E+10 to indicate missing data. When reading/writing MTZ files, the SFTOOLS MNF is converted from/to the CCP4 MNF definition respectively. It is crucial that proper MNFs are present. If you have missing data without MNFs, then you can introduce MNFs easily with the ABSENT command.

Asymmetric unit definition

Several commands need to know how the asymmetric unit is defined. The default is to use the CCP4 definition and it is highly recommended to stick with it (in the next release SFTOOLS will enforce adherence to the CCP4 definition). If you use a different definition then you can either convert to the CCP4 definition with the REDUCE command or you have to specify the definition each time you use a command that is definition dependent (this is very error prone, that is why it will be changed in the next release).

Input parsing

The program input is analyzed by a parser that divides the input into words. Words may be delimited by one or more spaces or any of the following characters ( ) , < > = [ ]. If you need to generate words including any of these characters or spaces (e.g. in a file name or column label) then the word(s) must be enclosed in double quotes.
Real numbers can be read in any format acceptable to FORTRAN, examples are: 1234 1234.5 1.2345E+3. Integers should be made up exclusively by digits 0 to 9 except for the first character which may be a minus sign. Character input is case insensitive except for file names.

The often used keyword COLUMN may be abbreviated to COL. Likewise, RESOLUTION may be replaced by RESOL. A more consistent method for abbreviating keywords will be implemented later.

Command arguments

It is advised for most commands to give the command name and its arguments on a single line. If you leave out the arguments 3 things can happen:

The subroutine uses default values

The program requests the missing information interactively

The program complaints and suggests that you read the help information

CCP4 compatibility

SFTOOLS is meant to adhere to the MTZ standard in all respects. However, the author does not use CCP4 extensively so there may still be some minor differences (please report them). Specific treatment of multi-record MTZ files is limited at this point. Most options will probably work fine with them but this has not been tested.
CCP4 supports maps of several types. SFTOOLS can read and write standard CCP4 electron density maps. The use of other map types has not been tested.

The user interface of SFTOOLS was developed independently of CCP4 practices and CCP4 parsing routines. Definitions of LABIN, LABOUT, HKLIN, HKLOUT and other common features of the CCP4 user interface are not supported. However, the user interface was designed for interactive use and should be easy to get used to. SFTOOLS can also prepare tabular data. Commands that prepare tables also allow the user some control over the table creation. In the next release of SFTOOLS this table control will be handled by a separate command. In the future tables may also support the use of XLOGGRAPH.

Summary and examples of major commands

Filling the data base

READ: Reading structure factor files
MAPIN: Reading electron density maps
SET: Creating the header

Saving (part of) the data base

WRITE: Writing structure factor files
MAPOUT: Writing electron density maps

Analyzing the data base

LIST: Listing the data base content
CHECKHKL: Data checking and statistics
COMPLETE: Checking data completeness
CORREL: Correlation coefficients between columns as function of resolution
PHASHFT: Phase shifts between phase columns as function of resolution
PLOT: Prepare tables with data for plotting
MAP: Get map statistics based on structure factors
MAPSTAT: Get map statistics based on a real map

Modifying the data base

ABSENT: Creating missing number flags
CALC: Perform column-based arithmetic (very important!)
SELECT: Selecting reflections (very important!)
DELETE: Delete columns or maps
PURGE: Delete reflections
EXPAND: Expand to lower symmetry space group
FFT: Create a map from structure factors
MAP2SF: Create structure factors from a map
HLCONV: Create Hendrickson Lattman coefficients from phase and figure of merit
I2F: Convert intensities to amplitudes
MAPLIMIT: Select a subsection of a map
REINDEX: Modify indices by matrix multiplication
RFREE: Select an RFREE set
SET: Modify header information
SORT: Sort the reflections
REDUCE: Reduce reflections to the asymmetric unit
MERGE: Merge reflections with identical indices.

Reading structure factor files

To read a structure factor file, SFTOOLS needs to know the name of the file, the format of the file, and the columns to be read. The name has to be supplied by the user. By default SFTOOLS reads all columns and it stores them in file order. However, the user can use the COLUMN keyword to control the columns to be read and their order in the data base. The file format will in most cases be determined from the file name extension, see below. If the format and extension do not match then the user can explicitly specify the format by a FORMAT keyword.

File format Extension FORMAT keyword

MTZ (CCP4) .mtz MTZ

MDF (OLD BIOMOL) .mdf MDF

BIOMOL ASCII FORMAT .snd SND

X-PLOR .xpl XPL

TNT .tnt TNT

Phases short format .31 31

Phases long format .31 31

XtalView fin format .fin FIN

XtalView phs format .phs PHS

XtalView double fin .df DF

Generic ASCII file .fmt FMT

In addition to reflection information, SFTOOLS also needs some header information. The MTZ format has the most complete header information and SFTOOLS needs most of it. If you read a non-MTZ file then SFTOOLS will prompt you for the missing header information. It is worthwhile to make an MTZ file for your project with just the header information in it. If you have to read a non-MTZ file then just first read in the MTZ with the header info and there will be no more questions asked.

SFTOOLS can read any generic ASCII file if:

There are no header lines

All reflections have the same format and number of columns

The indices H, K, and L are in columns 1, 2, and 3, respectively

Most ASCII files will be readable as is, however, if yours is not well-behaved then you can fix it as follows.

Use an editor or the Unix tail command to get rid of header lines:
tail +3 file_in > file_out
skips the first 2 lines.
Use the Unix awk command to force all reflections to have the same format or to place the indices in the first three columns:
awk '{printf("%4d%4d%4d%8.1f%8.1f",$3,$4,$5,$1,$2)}' file_in > file_out
swaps the order of the columns {1,2,3,4,5 to 3,4,5,1,2} and forces each line to have the same format.

For a detailed description see READ and Filling the data base

Examples

READ filename.mtz: Read all data from an MTZ file named filename.mtz
READ filename.mtz COL 3 4: Read columns 3 and 4 from an MTZ file named filename.mtz
READ filename.mtz COL 3 4 1 2: Read columns 1 to 4 from an MTZ file named filename.mtz but reverse the order of columns 1&2 and 3&4
READ filename.mtz COL NONE: Read only the header data from an MTZ file named filename.mtz
READ filename.mtz COL: Read data from an MTZ file named filename.mtz. SFTOOLS will list the label of each column and asks if it should be included
READ filename.hkl MTZ: Read all data from an MTZ file named filename.hkl
READ filename.xpl COLUMN Fcalc phase: Read "Fcalc" and "phase" columns from an XPLOR file named filename.xpl. SFTOOLS will ask for extra header information
READ header.mtz read filename.xpl: Read an XPLOR file named filename.xpl but now the header information will be taken from the header.mtz file

Reading electron density maps

To read an electron density file, SFTOOLS only needs to know the name of the file and the format of the file. The name has to be supplied by the user and in most cases the format can be determined from the file name extension, see below. If the format and extension do not match then the user can explicitly specify the format by a FORMAT keyword.

File format	Extension	FORMAT keyword
CCP4 map	.map	MAP
BIOMOL map	.mff	MFF
FRODO/O map (DSN6)	.dn6	DN6

SFTOOLS always reads the complete density map. Only one map can be in memory at any time. Use DELETE MAP to remove an old map before reading a new one. SFTOOLS will use the header information in the input map and will prompt the user for missing information.
CCP4 and BIOMOL maps can be sectioned in any order, however, SFTOOLS will internally always store the map in ABC order (sections along C and rows along B). For CCP4 maps not all map types may be supported, but the standard electron density maps should work.

Note: DSN6 files use only a single byte per grid point. It may be better to recreate your map from the map coefficients or to re-read the original MFF or CCP4 electron density file.

For a detailed description see MAPIN

Examples

MAPIN filename.map: Read a CCP4 electron density map
MAPIN filename.rho MAP: Read a CCP4 electron density map
MAPIN filename.dn6: Read a DSN6 electron density map

Creating the header

To enter the header information without reading it from a file you use the SET ALL command. The program will prompt you for the header information.

For a detailed description see SET

Examples

SET ALL: Fill in all header entries. SFTOOLS will ask you for the information
SET ALL write header.mtz: Fill in all header entries and write an MTZ file with just this information

Writing structure factor files

To write a structure factor file, SFTOOLS needs to know the name of the file, the format of the file, and the columns to be written. The name has to be supplied by the user. By default SFTOOLS writes all columns in the same order as they are stored in the data base. However, the user can use the COLUMN keyword to control the columns to write and their order in the output file. The file format will in most cases be determined from the file name extension, see the extensions table. In order to write a generic ASCII formatted file you have to specify the FORTRAN format string. It is absolutely required that the first 3 values are written as integers since these will be the indices. ALL other values MUST be written as reals because that is how they are stored in the program.

Some of the supported file formats are restricted in the number of columns and/or types of data that they accept. The user should use the COL keyword if needed to write the appropriate data. The requirements are detailed in the WRITE description.

For a detailed description see WRITE

Examples

WRITE filename.mtz: Write all data to an MTZ named filename.mtz
WRITE filename.hkl MTZ: Write all data to an MTZ named filename.hkl
WRITE filename.mtz COL Fscaled phase: Write columns with labels "Fscaled" and "phase" to an MTZ named filename.mtz
WRITE filename.mtz COL 3 4 1 2: Write columns 1 to 4 to an MTZ file named filename.mtz but reverse the order of columns 1&2 and 3&4
WRITE filename.mtz COL NONE: Write only the header data to an MTZ file named filename.mtz
WRITE filename.mtz COL: Write an MTZ file named filename.mtz. SFTOOLS will list the label of each data base column and ask if it should be written
WRITE filename.xpl COL 1 3 4: Write columns 1, 3 and 4 to an XPLOR file named filename.xpl
WRITE filename.hkl format(3i5,2f8.3) COL 1 2: Write columns 1 and 2 in the given format to an ASCII file named filename.hkl

Writing electron density maps

To write an electron density file, SFTOOLS only needs to know the name of the file and the format of the file. The name has to be supplied by the user and in most cases the format can be determined from the file name extension, see below. If the format and extension do not match then the user can explicitly specify the format by a FORMAT keyword, see the extensions table.

The current version of SFTOOLS always writes the complete density map. To write a subsection of the map you should use the MAPLIMIT command. In the next release the MAPLIMIT functions will be moved to the MAPOUT command in a more general way. By default, SFTOOLS will write a map in ABC order (sections along C and rows along B). For CCP4 and BIOMOL maps the user can specify a different order by adding the ORDER keyword.

For a detailed description see MAPOUT

Examples

MAPOUT filename.map: Write a CCP4 electron density map to a file named filename.map
MAPOUT filename.dn6: Write a DSN6 map for FRODO/O to a file named filename.dn6
MAPOUT filename.rho MAP: Write a CCP4 electron density map to a file named filename.rho
MAPOUT filename.mff ORDER A C B: Write a BIOMOL map to a file named filename.mff. Sections will be along the B axis and rows along the C axis)

Listing the data base content

The list command is used to list the actual contents of the data base. It accepts the following keywords: TITLE, LABELS, TYPE, CELL, SORT, SPACEGROUP, and REFLECTIONS. Each keyword limits the listing to the indicated information. If no keyword is given all information, except reflections, will be listed. Keywords can be abbreviated to the first 3 characters.

For a detailed description see LIST

Examples

LIST: List all header information
LIST CELL: List the unit cell parameters
LIST REF: List the reflection indices, resolution and first 6 columns
LIST REF COL 8 9: List the reflection indices, resolution and columns 8 and 9

Data checking and statistics

CHECKHKL reports potential problems with your data like: presence of systematically absent reflections, centric reflections with illegal phase, reflections outside asymmetric unit, multiple reflections with the same indices etc... It also lists for each column the average, minimum and maximum value, the minimum and maximum resolution, and the number of missing data. It is nice to keep the CHECKHKL output as part of the documentation of a new data set.

For a detailed description see CHECKHKL

Examples

CHECKHKL: Report problems and statistics

Checking data completeness

The COMPLETE command reports the completeness of your data as function of resolution. It can make bin-wise or cumulative tables and it can list percentage completeness as well as number of observed reflections. This option also reports a "100% criterium". This is the resolution in Angstrom of a 100% complete hypothetical data set with the same number of reflections as your data set. It is nice to keep the COMPLETE output as part of the documentation of a new data set.

The PDB keyword allows you to write a PDB file with pseudo-atoms for each observed and each absent reflection. Visualization with your favorite graphics program can tell you if data is randomly or systematically missing.

For a detailed description see COMPLETE

Examples

COMPLETE: Report bin-wise percentage completeness of first 10 columns
COMPLETE CUMULATIVE: Report cumulative percentage completeness of first 10 columns
COMPLETE COL 11: Report bin-wise percentage completeness of column 11
COMPLETE PDB: Create OBSERVED.PDB with reciprocal lattice as pseudo atoms

Correlation coefficients between columns

The CORREL command reports the correlation coefficient between two columns as function of resolution. It also gives an R-value but this only makes sense if the columns are on the same scale.

For a detailed description see CORREL

Examples

CORREL COL 1 3: Report correlation between columns 1 and 3

Phase shifts between phase columns as function of resolution

The PHASHFT command reports the average phase difference between two columns as function of resolution. The keyword COSINE can be used to list the cosine of the phase error.

For a detailed description see PHASHFT

Examples

PHASHFT COL 2 4: Report average phase difference between columns 2 and 4
PHASHFT COSINE COL 2 4: Report cosine of the phase difference between columns 2 and 4

Prepare tables with data for plotting

The PLOT command lists the bin-wise average of a column. Bins can be either as function of resolution or as function of another column. In the latter case the reflections are sorted by the other column before binning.

For a detailed description see PLOT

Examples

PLOT COL 1 VERSUS RESOL: Tabulate average value of col 1 in resolution bins
PLOT COL fobs VERSUS COL sigma: Tabulate average value of the column labeled "fobs" for bins of increasing values in the column labeled "sigma"

Get map statistics based on structure factors

The rms value of a map can be derived from the map amplitudes, i.e. it is independent of the phases. The correlation between two maps can be calculated when the structure factors of both maps are known (amplitudes and phases). In both cases it is not necessary to actually calculate the map.

For a detailed description see MAP

Examples

MAP RMS 1: Report the map rms based on structure factor amplitudes in column 1
MAP CORREL Fobs Pcalc Fcalc Pcalc: Report the correlation between two maps. Map 1 is defined by structure factors in columns with labels Fobs and Pcalc. Map 2 is defined by structure factors in columns with labels Fcalc and Pcalc. The phase column of the two maps does not have to be the same as in this example

Get map statistics based on a real map

After a map has been read or generated with the FFT command, the MAPSTAT command will list the header information and statistics for the map and individual sections.

For a detailed description see MAPSTAT

Examples

MAPSTAT: List the header info plus statistics for the map as well as for individual sections along the C-axis
MAPSTAT SECTION b: List the header info plus statistics for the map as well as for individual sections along the B-axis.

Creating missing number flags

If you have missing data then it is crucial for SFTOOLS that they are flagged by Missing Number Flags (MNFs). Old-style CCP4 programs relied on a SIGMA column being zero to indicated missing data. SFTOOLS will warn you when you read such an old-style file. Inserting proper MNFs is easy with the ABSENT command. The basic command structure is

ABSENT COL col_ids IF SELECTION

SELECTION can be any valid selection (see SELECT), whereas COL col_ids is a list of column labels or column numbers. MNFs are inserted in all listed columns for the reflections that fit the selection criterium. It is a good idea to give a SELECT ALL command prior to using the ABSENT command to make sure that all reflections will be used.

For a detailed description see ABSENT

Examples

ABSENT COL 1 2 IF COL 2 = 0: Set MNFs in columns 1 and 2 for reflections which have column 2 = 0
ABSENT COL 1 2 IF COL Iobs < 0: Set MNFs in columns 1 and 2 for reflections which have a negative value in the column with label Iobs

Perform column-based arithmetic

The CALC command is one of the most important commands and it gives you a lot of flexibility to accomplish non-standard tasks. Basically, the CALC command allows you to calculate a column of data based on existing data columns, constants, build-in functions and arithmetic operators. It is worth reading the rather extensive documentation for the CALC command.

For a detailed description see CALC

Examples

CALC R COL f_over_sigma = COL fobs COL sigma /: Create a column with label f_over_sigma which contains fobs / sigma
CALC R COL resolsq = resol 2 **: Create a column with label resolsq which contains the square of the reflection resolution (resol is a built-in function)
CALC F COL Fsimulated = COL Fcalc ran_g 10 * +: Create a column with label Fsimulated which contains the value of column Fcalc plus 10 times a random number from a Gaussian distribution with average = 0 and variance = 1
CALC (COL Fmap Pmap) = (COL Fcomplex Pnative) (COL Fnative Pnative) -: Create two columns labeled Fmap and Pmap which contain map coefficients for a Fcomplex - Fnative difference Fourier map

Selection of reflections

Just like the CALC command mentioned above, the SELECT command is very important to let you accomplish both common and advanced tasks. Basically the SELECT command allows you to select a subset of the reflections based on the reflection indices, data column values, and some special properties. Multiple SELECT commands can be combined to give even more control. For a full description of all options you will have to read the reference section.

For a detailed description see SELECT

Examples (many more options exist)

SELECT ALL: Select all reflections
SELECT COL 1 = ABSENT: Select all reflections with a MNF in column 1
SELECT INVERT: Invert the current selection
SELECT RESOL > 2.5: Select reflections with a resolution numerically greater then 2.5 (Note: this selects the lowest resolution data)
SELECT RESOL > 2.5 < 10.0: Select reflections in the resolution range from 2.5 to 10 Angstrom
SELECT COL fobs > COL sigma: Select reflections with a larger value in column fobs then column sigma
SELECT INDEX h = 0: Select reflections in the 0kl plane
SELECT INDEX l ZONE 2n + 1: Select reflections with an odd l index
SELECT INDEX h + k + l ZONE 2n + 1: Select reflections with h+k+l is odd
SELECT MULTI 3: Select reflections on a 3-fold axis
SELECT NOT MULTI 3: Select reflections that are not on a 3-fold axis
SELECT PHAERR: Select centric reflections with an invalid phase
SELECT SYSABS: Select reflections that should have been systematically absent
SELECT NONE SELECT PLUS INDEX h = 0 SELECT PLUS INDEX k = 0 SELECT PLUS INDEX l = 0 SELECT RESOL > 5: Select reflections with (H=0 or K=0 or L=0) and (resolution > 5 Angstrom)

Delete columns or maps

The DELETE command removes maps and data columns to free up space in the data base.

For a detailed description see DELETE

Examples

DELETE MAP: Delete the density map
DELETE COL 3 4: Delete columns 3 and 4

Delete reflections

The PURGE command removes reflections to free up space in the data base. Reflections to be removed should be deselected by the SELECT command prior to using purge. See SELECT for more information on the SELECT command.

For a detailed description see PURGE

Examples

PURGE: Delete all reflections that are currently not selected
PURGE NODATA: Delete all reflections that have MNFs in all columns

Expand to lower symmetry space group

Sometimes you may want to reduce the symmetry of your space group and explicitly generate the symmetry related reflections. In most cases you will want to expand to P1 and generate data for a full hemisphere of reciprocal space. The EXPAND command allows you to do this while updating your phase and/or Hendrickson-Lattman coefficients as needed. You can even expand to non-P1 space groups as long as it is a proper sub space group.

For a detailed description see EXPAND

Examples

EXPAND: Expand to P1
EXPAND 3: Expand to P2

Create a map from structure factors

The FFT command takes two columns with structure factors and uses them to create a density map using an in-memory fast Fourier transform. The structure factors will be left unchanged. The resulting map will cover exactly a full unit cell.

For a detailed description see FFT

Examples

FFT COL 1 2: Create a map based on structure factors in columns 1 and 2

Create structure factors from a map

The MAP2SF command inverts a density map to structure factors using an in-memory fast Fourier transform. The map must already be in memory before using the MAP2SF command and the map will be destroyed upon completion of the command.

For a detailed description see MAP2SF

Examples

MAP2SF: Invert the map held in memory and store the resulting structure factors in columns with labels COLUMN_###, where ### is the next available column number. This only generates structure factors for reflections that are already in the data base
MAP2SF COL Fmap Pmap: As above, but use column labels Fmap and Pmap instead
MAP2SF RESOL 2.5 COL Fmap Pmap: As above, but generate all reflections to 2.5 Angstrom resolution. (Even for reflections that were not yet present in the data base)

Create Hendrickson Lattman coefficients from phase and fom

The HLCONV command generates Hendrickson Lattman coefficients from the phase and figure of merit of a reflection. Because the latter represent a unimodal phase distribution, only the A and B coefficients are generated. You should not use this command if your phase and FOM were not derived from a unimodal distribution (e.g. heavy atom phasing). In that case use your original Hendrickson Lattman coefficients.

For a detailed description see HLCONV

Examples

HLCONV COL 2 3: Generate the A and B Hendrickson Lattman coefficients based on phases and fom in columns 2 and 3 respectively. The new columns will have labels PA and PB

Convert intensities to amplitudes

The I2F command takes two columns with an intensity and its sigma and produces two new columns with the amplitude and corresponding sigma. Negative intensities are set to MNFs. This command treats weak data reasonably, but it is recommended that you use the CCP4 TRUNCATE program.

For a detailed description see I2F

Examples

I2F col 1 2: Convert the intensity and its sigma in columns 1 and 2 to the amplitude and its sigma. The converted data is stored in columns with labels Fobs and Sigma-Fobs

Select a subsection of a map

The MAPLIMIT command allows you to select a subsection of a map. You can specify the new map limits as grid points, fractional, or orthogonal coordinates. Alternatively, you can give the name of a PDB file and the new limits will be set to cover the molecule.

NOTE: The current implementation does not allow the output map to exceed the length of a unit cell axis. This limitation will disappear in the next release of SFTOOLS.

For a detailed description see MAPLIMIT

Examples

MAPLIMIT GRID -12 34 0 56 3 29: Truncate the map so that it covers grid points -12 to 34 along x, 0 to 56 along y and 3 to 29 along the c axis.
MAPLIMIT PDB file.pdb PLUS 5: Truncate the map so that it covers the molecule in the pdb file with name "file.pdb" plus a 5 Angstrom boundary region.

Modify indices by matrix multiplication

The REINDEX command can be used to change the reflection indices. All indices will be multiplied by a user-specified matrix. It is up to the user to make sure the matrix is appropriate. The user will also have to update the cell parameters and or space group if needed. Phase columns and Hendrickson-Lattman coefficients will not be updated. The indices will be resorted and reduced to the CCP4 asymmetric unit.

For a detailed description see REINDEX

Examples

REINDEX MATRIX 1 0 0 0 0 1 0 1 0: Transforms H K L into H L K

Select an RFREE set

The RFREE command randomly selects a set of reflections to be used for the Rfree set. Alternatively, the user can ask for thin shells of reflections to be used for the Rfree set. The latter may be of interest in cases with high non-crystallographic symmetry. However, to get a reasonable number of shells, the individual shells are much thinner then one would like.

For a detailed description see RFREE

Examples

RFREE 2000: Select approximately 2000 reflections for the rfree set
RFREE 0.05: Select approximately 5% of the reflections for the rfree set
RFREE 0.05 SHELL: As above but select the reflections in thin resolution shells

Modify header information

All header information can be changed with the SET command. The keywords ALL, TITLE, LABELS, TYPES, SORT, CELL, and SPACEGROUP can be given to indicate which header item you wish to change. It is sufficient to type only the first 3 characters of each keyword.

For a detailed description see SET

Examples

SET ALL: SFTOOLS will prompt for all header information
SET CELL: SFTOOLS will prompt for the unit cell parameters
SET TYPES: SFTOOLS will prompt for all column types
SET TYP COL 3: SFTOOLS will prompt for the type of column 3

Sort the reflections

The SORT command can be used to sort the reflections by index, by resolution or by the value of one of the columns. This can be helpful if you want to look at your reflections with the LIST REF command.

For a detailed description see SORT

Examples

SORT: Sort the reflections with l changing fast, k intermediate and
SORT l k h: Sort the reflections with h changing fast, k intermediate and l changing slow
SORT RESOL: Sort the reflections by resolution. Highest resolution comes first
SORT RESOL DOWN: Sort the reflections by resolution. Highest resolution comes last
SORT COL 1: Sort the reflections by column 1. Lowest values of column 1 come first

Reduce reflections to the asymmetric unit

The REDUCE command forces all indices to be within the given asymmetric unit definition. By default the CCP4 definition is used and it is recommended not to deviate from that. Phases and Hendrickson-Lattman coefficients will be updated if necessary.

For a detailed description see REDUCE

Examples

REDUCE: Force all indices to obey the CCP4 asymmetric unit definition
REDUCE TNT: Force all indices to obey the TNT asymmetric unit definition

Merge reflections with identical indices.

The MERGE command merges reflections with identical indices. With the exception of multi-record MTZ files, this situation should not occur. In some benign cases the multiple reflections contain identical information in all columns or only one reflection contains valid data for any one column (the rest has MNFs). In the latter case the MERGE command can be applied safely. If two or more reflections contain non-identical data for one or more columns then you can force merging by averaging by giving the MERGE AVERAGE command. However, you most likely have a major problem with your data and MERGE AVERAGE should only be used if you know what caused the problem.

For a detailed description see MERGE

Examples

MERGE: Merge reflections if it is "safe"
MERGE AVERAGE: Merge reflections by averaging

Command reference section

Following is the list of on-line help information. You can get this during interactive use by typing the name of the command followed by the keyword "HELP". E.g. ABSENT HELP will give you the help information for the ABSENT command.

The available keywords/commands are:

ABSENT, CALC, CHECKHKL, COMPLETE, CORREL, DELETE, EXPAND, FFT, FOURPT, FULLMDF, FULLMTZ, HLCONV, I2F, LIST, MAP, MAP2SF, MAPIN, MAPLIMIT, MAPOUT, MAPSTAT, MERGE, MODE, OPTION1, PHASHFT, PLOT, PURGE, READ, REDUCE, REINDEX, RFREE, SELECT, SET, SORT, STOP, WINDOW, WRITE

ABSENT

  OPTION: ABSENT COL col_ids IF COL col_id = 0
  ============================================

  Option to generate Missing Number Flags (MNFs)

  This command will set the values in the columns
  specified by col_ids to absent if the value in
  the column specified by col_id is zero. A column
  identifier can be either the column number or the
  column label.
  The part following the IF keyword can actually be
  any valid selection expression (give SELECT HELP
  for more information on selection expressions)
  Reflections that are already deselected due to a
  previous SELECT command will not get any MNFs
  Also note that after this command a SELECT ALL
  command will be issued automatically.

  EXAMPLES:(assuming column 2 has label sigma)

  ABSENT COL 1 2 IF COL 2 = 0
  ABSENT COL 1 2 3 4 IF COL sigma = 0
  ABSENT COL 3 4 IF RESOL > 3.0

CALC

  OPTION: CALCulate  RESULT = expression
  ======================================

  Command to perform arithmetic on data columns.
  The expression is evaluated and stored in the
  column(s) indicated by result.

  The expression may contain operands and
  operators and should follow the Polish notation.
  This means that first the operands are given and
  then the operator. (e.g. 5+3 becomes 5 3 +). It
  is the users responsibility to assure that the
  correct number of operands are given for each
  operator (see list below). Operands may either be
  a value, a column_id or some kind of function
 - VALUE : integer, real or complex value. Complex
           values consisting of an amplitude and
           phase must be enclosed in parentheses
           e.g. i=(1.0 90.0) or square brackets if
           they represent the real and imaginary
           parts. e.g. i=[0.0 1.0].

 - COLUMN: A COLumn keyword followed by 1 or 2
           column_ids (numbers or labels). Give
           1 column_id if you wish to use the value
           in that column. Give 2 column_ids if the
           columns contain complex data. Enclose
           the keyword and the ids in parentheses
           if the columns contain an amplitude and
           a phase. Use square brackets if they
           contain the real and imaginary parts.
           If a column value is absent then the
           whole expression evaluates to absent.

 FUNCTION  one of the following built-in functions

 - C     : This evaluates to 0 for centric and to
           1 for acentric reflections
 - M     : This evaluates to the reflection
           multiplicity (e.g. 2 on two-fold etc)
 - P     : This evaluates to the phase restriction
           for centric reflection or MNF for
           non-centrics
 - H     : Returns the H-index for this reflection
 - K     : Returns the K-index for this reflection
 - L     : Returns the L-index for this reflection
 - RAN_U : Return a random number from a uniform
           distribution between 0 and 1. The set of
           random numbers depends on a seed value
           which is 1234 by default. To modify the
           seed value (and hence get a novel set of
           random numbers) you must issue a command
           CALC SEED number
           where number can be any positive integer
 - RAN_G : Return a random number from a Gaussian
           distribution with mean 0 and variance 1
           (see RAN_U for the SEED value)
 - RFREE(r)
           Randomly returns 0 and 1 values for use
           in RFREE for XPLOR. If 0 < r < 1 then r
           represents the fraction of data to use
           for the free R-factor. If r > 1 then it
           represents the absolute number of
           reflections to use.
 - STOL  : This evaluates to sin(theta/lambda)
 - STOLSQ: This evaluates to sin(theta/lambda)**2

  RESULT : Indicates where to store the result of
           the expression. RESULT can be:
  TYPE COLumn c1, (COLumn c1 c2), [COLumn c1 c2]
  In the first case a result is stored in column c1
  The column type will be set to TYPE or to R if no
  type is specified.
  In the second case a complex result is stored in
  columns c1 and c2 as an amplitude and phase resp.
  The column types are set by the program. In the
  third case, the complex result is stored as the
  real and imaginary parts resp. again with the
  column types set automatically.
  The result columns are created if necessary

  OPERATOR (REAL OPERANDS, COMPLEX OPERANDS)

      + (2,4) : Summation
      - (2,4) : Subtraction
      * (2,4) : Multiplication
      / (2,4) : Division
     ** (2,3) : Power. The base may be complex, the
                exponent not (it can be any! real)
    SIN (1,-) : Sine
    COS (1,-) : Cosine
    TAN (1,-) : Tangent
    DTR (1,-) : Convert from degrees to radians
    RTD (1,-) : Convert from radians to degrees
    ABS (1,2) : Absolute value. For complex values
                this is the complex vector length
     LN (1,-) : Natural logarithm
    EXP (1,-) : Exponent
    MIN (2,4) : Minimum of two values
    MAX (2,4) : Maximum of two values

  EXAMPLES:
  (assume the data base contains 4 columns named; fobs, sigma, fcalc and phase)
  CALC COL sigma = 0
    set column sigma to 0
  CALC COL sigma = COL fobs 10 /
    set sigma to fobs/10. The result column will
    keep column type Q
  CALC COL F/sigF = COL 1 COL 2 /
    make a column labeled F/sigF and store fobs
    over sigma in it. The result column will get
    column type R
  CALC COL stol = stol
    make a column labeled stol and store sin(theta)
    over lambda in it for each reflection
  CALC COL resol = 0.5 stol /
    create a column labeled resol and store the
    resolution in Angstrom {1/(2*stol)}
  CALC COL 5 = m
    make a column labeled COLUMN_005 and store the
    multiplicity for each reflection, e.g. 6 for
    00L reflections in hexagonal space group.
  CALC COL 7 = m
    identical including label COLUMN_005
  CALC COL centric = 1 c -
    make a column labeled centric that contains 0
    for acentrics and 1 for centrics
  CALC COL fcalc = COL fcalc ran_g 100 * +
    ran_g returns a random number from a Gaussian
    distribution. Multiply this by 100 to get a
    mean of 0 and variance of 100 (st. dev. of 10)
    and then add it to your fcalc
  CALC q COL newsigma = 2 COL sigma *
    make column with label newsigma twice the value
    found in column sigma. Set the label of the new
    column to Q!!!
  CALC (COL Fnew Pnew) = (COL 1 4) (COL 3 4) -
    create columns Fnew and Pnew and store in it
    fobs - fcalc as amplitude and phase.
    Column types are set to F and P
  CALC [ COL real imag ] = (COL 3 4)
    convert fcalc and phase to real and imagenary
    components and stored these in columns labeled
    real and imag, column types are set to R and R
  CALC COL test = rfree(0.05)
    select 5% of the reflections for XPLOR RFREE
  CALC COL test = rfree(3500)
    select 3500 reflections for XPLOR RFREE

CHECKHKL

  OPTION: CHECKHKL [ASUNIT]
  =========================

  Command to check the reflection indices. It will
  report the following:
  - number of reflections outside asymmetric unit
  - number of centrosymmetric reflections
  - number of unallowed reflections
  - number of reflections found on the crystallo-
    graphic symmetry axes

  ASUNIT  Asymmetric unit specification by:
  CCP4    Keyword to use CCP4 definition (default)
  BIOMOL  Keyword to use BIOMOL definition
  TNT     Keyword to use TNT definition
  MATRIX m11 m12 m13 m21 m22 m23 m31 m32 m33
          Give REDUCE HELP to get more information
          on how to define the asymmetric unit by
          the MATRIX keyword

COMPLETE

  OPTION: COMPLETE [SETTINGS] [MODE] [ASUNIT] [COLUMN]
  ====================================================

  Command to list the data completeness. Only the
  reflections within the asymmetric unit are used.

  SETTINGS is one of the following:
  SHELLS n   Display data in n shells (n is saved)
  RESOL  r   Set maximum resolution [A] (default is
             the maximum observed resolution)

  MODE is one of the following:
  NUMBERS    list the number of reflections in each
             resolution bin. The default is to
             print the completeness in percentage
  CUMULATIVE list the cumulative completeness. The
             default is to list in resolution bins
  PDB        Make PDB file OBSERVED.PDB in which
             OBS & ABS residues indicate observed
             and absent reflections in rec. space
             Observed reflections will have their
             B-value set to the value in column 1
             (Nice if column 1 contains F/SIGF)
  TABLE      Keyword. When given, the contents of
             the table will be written to the file
             COMPLETE.TAB (without header & totals)

  ASUNIT  Asymmetric unit specification by:
  CCP4    Keyword to use CCP4 definition (default)
  BIOMOL  Keyword to use BIOMOL definition
  TNT     Keyword to use TNT definition
  MATRIX m11 m12 m13 m21 m22 m23 m31 m32 m33
          Give REDUCE HELP to get more information
          on how to define the asymmetric unit by
          the MATRIX keyword

  COLUMN  By default, COMPLETE will list the
          completeness of the first 10 columns. The
          COLUMN keyword can be used to specify up
          to 10 specific columns.

  EXAMPLE: COMPLETE COL 1 3 5
  (list the completeness of columns 1, 3 & 5)

  Data completeness cannot be caught in a single
  number and resolution limits reported in the
  literature strongly depend on criteria unknown to
  the reader. A more objective (still not ideal)
  specification would be to state: the number of
  observed reflections corresponds to a 100%
  complete dataset to X angstrom resolution. a good
  estimate of the value X is given by SFTOOLS

CORREL

  OPTION: CORREL [COLUMN c1 c2] [SETTINGS] [TABLE]
  ================================================

  Command to calculate the correlation and R-factor
  between two columns.

  COLUMN      Keyword which is followed by
  - c1 c2     2 column-id''s, names or numbers

  SETTINGS changes the table layout as follows:
  SHELLS      Keyword followed by
  - nshell    displays data in nshell shells
  RESOLUTION  Keyword followed by
  - rmin rmax Resolution limits [A] (e.g. 10 2)

  TABLE      Keyword. When given, the contents of
             the table will be written to the file
             CORREL.TAB (without header & totals)

  The column labels of the table are:

  NSHELL     Number of resolution shell
  DMIN DMAX  Minimum/maximum resolution
  RFACT      Rfactor in percent
             ( 200*Sum|col1-col2|/sum(col1+col2) )
  CORREL     Correlation coefficient
  F1 F2      Average value of col1 and col2 in the
             resolution bin
  NREF       Number of reflections used for the
             statistics

DELETE

  OPTION: DELETE [COLUMN col_ids] [MAP]
  =====================================

  Command to remove information from the data base
  COLUMN   : Keyword that is followed by column-id
             Label(s) or number(s) to identify the
             column(s) that will be deleted
  MAP      : Keyword to indicate that the map has
             to be deleted

  EXAMPLES:

  DELETE COLUMN 5 6
  DELETE MAP

EXPAND

  OPTION: EXPAND [SPAGRP] [SILENT] [ASUNIT]
  =========================================

  Expand the reflections to lower symmetry.
  Phase information will be treated, the spacegroup
  information will be updated and the expanded.
  Reflections will be sorted.

  SPAGRP Space group number to which to expand. This
         must be a proper subgroup of the original
         space group (default is 1)
  SILENT Keyword to suppress output
  ASUNIT Asymmetric unit specification which is:
  CCP4   Keyword for CCP4 definition (default)
  BIOMOL Keyword for BIOMOL definition
  TNT    Keyword for TNT definition
  MATRIX Keyword followed by 9 integers specifying
         the asymmetric unit. Give REDUCE HELP for
         more details on the MATRIX definitions

  WARNING: if you expand to a SPACEGROUP that has
  its origin at a different position then the
  phases will not be correct (e.g. P212121 to P21)

  EXAMPLES:

  EXPAND           (expand to P1)
  EXPAND 3         (expand to P2)

FFT

  OPTION: FFT COL id1 id2 [STEP x] [GRID nx ny nz]
  ================================================

  Calculate a map based on the Fourier coefficients
  in columns id1 (amplitude) and id2 (phase).
  All active reflections are used. To restrict the
  data to a certain resolution use option SELECT.

  STEP  Force the program to use a grid size that
        is as close to x Angstrom as allowed
  GRID  Force the program to use nx, ny and nz
        grid points along the a, b and c axes
        respectively. The numbers must be multiples
        of 2, 3 and 5 and nx must be positive. If
        an illegal number is given the next valid
        number will be used

  If neither STEP nor GRID are specified the grid
  size defaults to 1/3 of the max. resolution

  Note: If your amplitudes are on absolute scale
  your map will be on absolute scale as well

  EXAMPLES
  ========

  FFT COL fobs pmir
  FFT COL 1 2
  FFT COL 1 2 GRID 96 60 81
  FFT COL 1 2 STEP 0.8

FOURPT

  OPTION: FOURPT MAPTYPE COLUMNS
  ==============================

  Command to generate Fourier coefficients for
  several standard transforms.

  MAPTYPE must be one of the following numbers:
   0 = ( F1 -  F2),P1      : Fo-Fc-map
   1 = (2F1 -  F2),P1      : 2Fo-Fc-map
   2 = (3F1 - 2F2),P1      : 3Fo-2Fc-map
   3 = |F1|,P1 + |F2|,P2
   4 = |F1|,P1 - |F2|,P2
   5 = |F1|,P1             : Straight Fourier
   6 = |F1|**2             : Patterson
   7 = (F1-F2)**2          : Patterson
   8 = |F1|*|F2|,(P1-P2)   : Phased trans. function
   9 = |F1|*|F2|,(-P1-P2)  : Phased trans. function

  COLUMNS is the COL keyword followed by column
  specifications. The columns have to be specified
  in the order in which they occur in the formulae
  F1 and F2 represent amplitude columns. P1 and P2
  represent phase columns. The map coefficients are
  stored in 2 new columns with labels FMAP and PMAP
  (amplitude and phase respectively). The Patterson
  map options generate only one column with label
  FPAT. If a dummy phase column with zeroes is
  required you could make it with the command:
  CALC COL PPAT = 0
  If you wish to weight your coefficients with a
  figure of merit you can do so with the command
  CALC COL FMAP = COL FMAP COL FOM *

  EXAMPLE: FOURPT 1 COL fobs fcalc pcalc

FULLMDF


  NOTICE: Option FULLMDF will become obsolete in the next release and
          will no longer be supported. Try to avoid using it in scripts.

  OPTION: FULLMDF
  ===============

  This option converts a CCP4 MTZ into a BIOMOL MTZ
  In the first step the user must indicate how to
  generate absence flags.
  If a column with anomalous data is found (column
  type = D) then user input will also be requested
  to convert the anomalous data.
  The conversion between asymmetric unit definitions
  will be made automatically.

FULLMTZ


  NOTICE: Option FULLMTZ will become obsolete in the next release and
          will no longer be supported. Try to avoid using it in scripts.

  OPTION: FULLMTZ
  ===============

  This option automatically replaces absence flags
  (-1E+10) by zeroes.

  If a column with anomalous data is found (column
  type is D) then user input will be requested if
  and how the anomalous data has to be converted

  Indices will be reduced to the CCP4 asymmetric
  unit automatically

HLCONV

  OPTION: HLCONV COL phase fom
  ============================

  Given a phase and figure of merit, this command
  will generated the A and B Hendrickson-Lattman
  coefficients. PLEASE NOTE that this is only
  advisable if your source of phase information
  is unimodal. If you have heavy atom phases then
  you SHOULD use the original bimodal phase
  distributions derived from them. This option
  may be useful to generate HL coefficients for
  phased refinement with XPLOR or REFMAC, based
  on FOM and phases from a map after density
  modification

  Example:
  HLCONV col 2 3

I2F

  OPTION: I2F COL I SIGI
  ======================

  Command to convert intensities plus their
  sigmas to amplitudes and corresponding sigmas.
  The argument consists of the keyword COL
  followed by the column labels (or numbers) of
  the columns containing I and SigI respectively

  Example: I2F COL 1 2
  Example: I2F COL Iobs Sigma-I

  The results are stored in columns with labels
  Fobs and Sigma-Fobs. NOTE: if columns with these
  labels exist then they will be overwritten !!!
  The I2F conversion is calculated as:

  Fobs = SQRT(Iobs)
  Sigma-Fobs = SQRT( SQRT( Iobs**2 + 0.5*Sigma-I**2) - I)


  NOTE: it may be better to use the CCP4 program
  TRUNCATE for this step since it treats negative
  and very weak data more elegantly (I2F flags
  negative data as absent!!!)

LIST

  OPTION: LIST [ITEMS]
  ====================

  Command to list header information
  -ITEMS is a list of header items to be shown
   (it suffices to give the first 3 characters)
   The default is to list all header items

   TITLE        title cards
   LABELS       column labels, numbers and types
   TYPE         column labels, numbers and types
   CELL         unit cell parameters
   SORT         sort order
   SPACEGROUP   space group related data

   REFLECTIONS  reflection data. This argument.
                can be followed by COL and one to
                six column specifiers

   Example: LIST REF col 1 2 11 12
            LIST SPA CELL
            LIST

MAP

  OPTION: MAP RMS F1 [SHELLS n]
  OPTION: MAP CORREL F1 P1  F2 P2 [SHELLS n]
  ==========================================

  Option to calculate the r.m.s. of a map based
  on the amplitude of its coefficients or to
  calculate the correlation coefficient between
  two maps given the coefficients for both maps.
  The statistics will be listed as function of
  resolution.

  RMS    Keyword to calculate the map r.m.s.
         based on the amplitude in column F1

  CORREL Keyword to calculate the correlation
         coefficient. F1 P1 and F2 P2 are the
         column specifiers for the coefficients
         of map 1 and map 2 respectively

  SHELLS n   Keyword followed by the number of
             shells to use in the analysis.
             The given value will become the new
             default. The original default is 20


  You can give only one keyword at a time, but
  if you give the CORREL keyword the program
  will automatically give you the r.m.s. values
  of the two maps being correlated

  EXAMPLE:

  MAP RMS 1
  (rms of a map based on amplitudes in column 1
  MAP CORREL fobs pmir faveraged paveraged
  (correlation between mir map and averaged map)
  MAP CORREL 1 2 5 6 SHELLS 10
  (As before but list only 10 resolution shells)

MAP2SF

  OPTION: MAP2SF [RESOL r] [F000] [COL id1 id2]
  =============================================

  Calculate Fourier coefficients from a map. The
  map to be transformed already has to reside in
  memory. You will always get coefficients for all
  reflections that are already in the data base
  (even if they are unselected).

  RESOL r
  This keyword indicates that ALL legal reflections
  (except F000) to a resolution of "r" Angstrom
  will be stored. The default is to store only the
  reflections for which there is already an entry
  in the data base. If there are no reflections in
  the data base and RESOL is not specified, then
  all legal reflections to a resolution of 3 times
  the largest grid spacing are calculated

  F000
  If given this indicates that F000 should also be
  kept (WARNING, many programs, potentially incl.
  SFTOOLS, do not like the infinite resolution of
  F000).

  COL id1 id2
  If id1 and id2 are text labels, then id1 and id2
  are given to the new amplitude and phase columns
  If id1 and id2 are numbers of existing columns
  then the new amplitude and phase columns will
  overwrite the id1 and id2 columns. If the COL
  keyword is not given then SFTOOLS will create 2
  columns with COLUMN_NNN labels where NNN is the
  column number

  Note: If your map is on absolute scale then the
  Fourier coefficients will be as well

  EXAMPLES
  ========

  MAP2SF
  MAP2SF COL Fnew Pnew
  MAP2SF RESOL 2.0 col 3 4
  MAP2SF RESOL 3 F000 col 3 4

MAPIN

  OPTION: MAPIN FILENAME [FORMAT]
  ===============================

  Command to read in an electron density file.

  FILENAME    is the name of the file. The program
    will try to deduce the file format from the
    extension. It will recognize .mff, .map, .dn6
  FORMAT      can be one of the following:
    MFF, MAP, DN6
    This overrules the file name extension format

  File formats are:
  MFF   BIOMOL format
  MAP   CCP4 real*4 format
  DN6   FRODO / O map format

  NOTE: DN6 maps for hardware other then SGI may not
        be compatible with SFTOOLS. Please let me
        know about problems

  EXAMPLE:

  MAPIN file.mff
  MAPIN file.map
  MAPIN file.dn6
  MAPIN file.rho MFF

  Notes:
  The input map can be in any order. However it is
  stored internally in A-B-C order. There can only
  be one map in memory. An existing map has to be
  deleted before reading a new one (DELETE MAP)

MAPLIMIT


  NOTICE: Option MAPLIMIT will become obsolete in the next release and
          will no longer be supported. Try to avoid using it in scripts.
          In the next release the functionality of MAPLIMIT will be
          moved to the MAPOUT command. This allows a fully general and
          robust implementation.

  OPTION: MAPLIMIT TYPE value(s)
  ==============================

  Command to restrict a map to certain limits.
  The limits can be specified in various ways as
  indicated by the TYPE keyword which can be one
  of the following:

  PDB filename PLUS r
    This returns a block of density that surrounds
    the atoms in the PDB file leaving an extra
    "r" Angstrom on all sides. If "PLUS r" is not
    specified a default of 5 Angstrom is used

  GRID a_l a_u b_l b_u c_l c_u
    This returns a block of density with lower and
    upper limits along a, b and c as given in grid
    coordinates

  FRACT a_l a_u b_l b_u c_l c_u
    This returns a block of density with lower and
    upper limits along a, b and c as given in
    fractional coordinates

  ORTHO a_l a_u b_l b_u c_l c_u
    This returns a block of density with lower and
    upper limits along a, b and c as given in
    orthogonal (Angstrom) coordinates

  EXAMPLES:

  MAPLIMIT PDB protein.pdb PLUS 4
  MAPLIMIT FRACT 0 0.5 0 0.5 0 0.5
  MAPLIMIT GRID -5 34 0 60 12 49

  Notes:
  Every gridpoint in the new map must be present in
  the current map. It is allowed to go outside the
  unix cell, but none of the new axes can be larger
  than a full unit cell axis. E.g. if the a-axis
  runs from 0 to 99, you can ask for the subset
  -5 to 20, but not -5 to 99

MAPOUT

  OPTION: MAPOUT FILENAME [FORMAT] [ORDER a b c]
  ==============================================

  Command to write a electron density file.

  -FILENAME is the name of the file. The program
   will try to deduce the file format from the
   extension. It will recognize .mff, .map, .dn6
  FORMAT   can be one of the following:
   MFF, MAP, DN6
   This overrules the file name extension format
  ORDER   By default the map is written with
          sections along C, rows along B and grid
          steps along A (ORDER A B C). By giving
          different permutations of A B C you can
          change the map layout.

  File formats are:
  MFF   BIOMOL format
  MAP   CCP4 real*4 format
  DN6   FRODO / O map format

  NOTE: I have only created DN6 maps for display on SGI
        If you use it on different hardware then please
        let me know if it works or not.

  EXAMPLE:

  MAPOUT file.mff
  MAPOUT file.map
  MAPOUT file.dn6
  MAPOUT file.rho MFF
  MAPOUT file.map ORDER A C B
  (sections along B, rows along C)

MAPSTAT

  OPTION: MAPSTAT [SECTION a b c]
  ===============================

  Command to list header and statistics of the
  current map. Statistics are given per section
  and for the whole map. You can specify which
  axis to use as sectioning axis by the SECTION
  keyword followed by the required sectioning
  axis. If no SECTION keyword is given then
  sections will be along the C-axis

  EXAMPLES:

  MAPSTAT
  MAPSTAT SECTION a
  MAPSTAT SECTION b

MERGE

  OPTION: MERGE MODE
  ==================

  Command to merge reflections with identical
  indices. There are two modes:
  SAFE     Reflections are only merged if none of
           the columns has valid data entries in
           more than one reflection [default]
  AVERAGE  Merging is done by taking the average
           of the reflections

  MERGE merges multiple reflections with identical
  HKL, it does not merge different columns!!!
  The AVERAGE option exists, but you should never
  need to use it. If you need it you probably have
  some kind of problem with your data

  EXAMPLES:

  MERGE SAFE
  MERGE AVERAGE   (if you know what you are doing)

MODE


  NOTICE: Option MODE will become obsolete in the next release and
          will no longer be supported. Try to avoid using it in scripts.

  OPTION: MODE BATCH | INTERACTIVE
  ================================

  Bring the program in or out of Batch mode
  Use MODE BATCH when running SFTOOLS in batch
  This suppresses some questions by SFTOOLS, e.g.
  to hit return to see the next page in LIST REF
  Use MODE INTERACTIVE to return to interactive
  mode if that would ever be useful

  EXAMPLES:

  MODE BATCH
  MODE INTERACTIVE

OPTION1


  NOTICE: Option MODE will no longer be supported in the next release.
          If you want to add your own options please contact me.

  OPTION: OPTION1 ....
  ====================

  Option1 is a dummy option that provides a means
  for users to add their own option. To do so,
  insert your code in this subroutine and modify
  this help text. If you wish to give the option a
  more sensible name then you have to modify the
  calling sequence in the main routine, the name
  in routine lstopt and of course the name in the
  subroutine header and in the last write statement

  If you plan to do some major programming, then it
  might be wise to contact me first, since your
  option might already exist in my experimental
  version. In addition I could supply you with a
  makefile and some other goodies

  If your option is of general interest, then you
  are urged to return the source code to me so that
  it can be implemented in the official release

  Bart Hazes, e-mail bart@mycroft.mmid.ualberta.ca, bart@mrc-lmb.cam.ac.uk

PHASHFT

  OPTION: PHASHFT [COL c1 c2] [SETTINGS] [TABLE] [COSINE]
  =======================================================

  Command to calculate the average phase difference
  between two columns of data.

  COLUMN      Keyword followed by
  - c1 c2     2 column-id''s, names or numbers

  SETTINGS changes the table layout as follows:
  SHELLS      Keyword followed by
  - nshell    Displays data in nshell shells
  RESOLUTION  Keyword followed by
  - rmin rmax Resolution limits [A] (default is to
              use the observed resolution limits)

  TABLE     Keyword. When given, the contents of
            the table will be written to the file
            PHASHFT.TAB (without header & totals)

  COSINE    Keyword to instruct the subroutine to
            list the cosine of the phase difference
            (Default is degrees)

PLOT

  OPTION: PLOT COL c1 VERSUS [RESOL] [COL c2]
  ===========================================

  Command to create a plot file with the binwise
  averages of column c1 on the y-axis. The x-axis
  can be either resolution bins or bins of values
  found in column c2.

  COL c1   Column keyword followed by column name
           or number

  VERSUS   Keyword to be typed literally

  RESOL    Keyword to be typed literally if you
           wish to plot as function of resolution

  COL c2   Column keyword followed by column name
           or number. The data in column c1 will
           be given as function of the data in
           column c2

  SHELLS n Keyword followed by the number of bins

  EXAMPLE: plot col fobs versus col sigma

  The output file (PLOT.DATA) has 5 columns
  - The lower limit of the bin
  - The upper limit of the bin
  - The midpoint of the bin
  - The average of col c1 for the bin
  - The number of reflections in the bin

PURGE

  OPTION: PURGE [SELECT] [NODATA] [YES]
  =====================================

  Command to delete records. Records to be deleted
  must first be deselected by command SELECT.
  Command SELECT may be given from the main menu
  or optionally from within PURGE. For help on
  SELECT, type SELECT HELP from the main menu

  YES     Keyword to indicate that no confirmation
          should be requested. By default, PURGE
          will ask a confirmation before starting
          Keyword yes must appear before select

  NODATA  Keyword to indicate that all reflections
  which have absent flags in all columns should be
  deleted

READ

 OPTION: READ FILENAME [FORMAT] [COLUMN columns]
 ===============================================

 Command to read a structure factor file.

 -FILENAME is the name of the file. The program
  will try to deduce the file format from the
  extension. It will recognize .mtz, .mdf, .snd,
  .xpl, .tnt, .31, .fin, .phs, .df, and .fmt
 FORMAT can be one of the following: MTZ, MDF,
  SND, XPL, TNT, 31, FIN, PHS, DF or FMT
  This overrules the file name extension format
 COLUMN Keyword to select specific columns
  Columns can be specified by numbers or labels
  (also mixed), and in any order. The order of
  columns in SFTOOLS will reflect the specified
  order and not the order on the MTZ. A column
  may even be listed more than once!
  If no columns are given, then the program will
  ask the user for each column  whether or not
  to include it. If no COLUMN keyword is given
  all columns are read
  THE COLUMN KEYWORD MUST BE THE LAST ARGUMENT !

 File formats are:
 MTZ   CCP4 format
 MDF   old BIOMOL format
 SND   BIOMOL ascii format
 XPL   XPLOR format
 TNT   TNT format
 31    PHASES short and long binary formats
 FIN   Xtalview fin-format
 PHS   Xtalview phs-format
 DF    Xtalview double fin-format
 FMT   File in arbitrary ASCII format

 NOTE: All formats except MTZ may need additional
 header information. The program will request this
 information interactively if necessary. All but
 the MTZ, MDF, SND and FMT formats have certain
 restrictions on the number, order, and type of
 columns. It is the users responsibility to use the
 COLUMN keyword to read the appropriate number and
 types of columns. SFTOOLS will check that you
 obey these restrictions.

 EXAMPLES:

 READ myfile.mtz
 (read all columns of myfile.mtz in mtz format)

 READ myfile.hkl MTZ COLUMN 3 1 2
 (read columns 1, 2 and 3 of myfile.hkl in mtz
 format. Column 3 will be column 1 in SFTOOLS)

 READ myfile.mtz COL
 (read myfile.mtz in mtz format and ask for each
  column whether or not it should be read)

 READ myfile.fmt
 (read the ASCII file myfile.fmt The program will
  figure out the format for you based on the first
  line(s) of the file. It will ignore character
  data amidst reflection data but you must edit
  out header lines (try the unix TAIL command).
  Also, all lines must have the same format as the
  first line(s). The program will ask you how many
  lines each reflection uses so that it can handle
  reflections that span more than one line. It
  also asks you how phase information is encoded
  Your file must contain the indices in the first
  three data columns (preceding character data is
  no problem though). If this is not the case then
  you can use the unix AWK command to fix it.
  The following awk command would correct a file
  which has the indices in columns 3, 4 and 5

  awk '{printf("%4d%4d%4d%8.1f%8.1f",$3,$4,$5,$1,$2)}' file_in > file_out

  One last note: if your file contains missing
  data in some manner (e.g. Sigma=0) then you will
  have to use the ABSENT command to insert proper
  missing number flags (MNFs) for these reflections

REDUCE

  OPTION: REDUCE [SILENT] [ASUNIT]
  ================================

  Command to reduce reflections to the asymmetric
  unit. Phases & Hendrickson/Lattman coefficients
  (if present) will be updated

  SILENT  Keyword to suppress output
  ASUNIT  Asymmetric unit definition which can be:
  CCP4    Use CCP4 definitions (default)
  BIOMOL  Use BIOMOL definitions
  TNT     Use TNT definitions
  MATRIX  Keyword followed by 9 integers i1-i9
          which define a packing matrix definition

  The asymmetric unit is defined as the set of
  reflections which maximize:
  (i1*h+i2*k+i3*l)*1024**2+(i4*h+i5*k+i6*l)*1024+
   i7*h+i8*k+i9*l

  Example: P4 hkl:h>=0,l>=0 0kl:k>=0 h>0:k>0
  MATRIX  0 0 1  1 1 0  0 1 0
  0 0 1 selects the hemisphere L>=0
  1 1 0 selects the quadrant H+K>=0
  0 1 0 selects the 0kl instead of h0l

  EXAMPLE:
  REDUCE CCP4
  Reduces all indices to the asymmetric unit defined by CCP4

REINDEX

  OPTION: REINDEX [MATRIX]
  ========================

  Command to transform the indices.
  MATRIX  Keyword followed by 9 numbers specifying
          the transformation matrix (row-wise). The
          program does not check the validity of
          the matrix and phases will not be changed
          The user also has to update the header
          manually if required

  After the transformation, the data are resorted

  EXAMPLE:
  REINDEX MATRIX 1 0 0  0 0 1  0 1 0
  Transforms H K L into H L K

RFREE

  OPTION: RFREE nr_of_rfree [SHELL [width]]

  NOTE: this subroutine uses the CCP4 definition
  of RFREE data with 0=test set and 1=working set
  When you write out an XPLOR file then these flags
  are automatically converted to the reverse
  definition of XPLOR. A future version will also
  allow flags > 1 for multi-set RFREE flags

  Create a column named RFREE with values set to 0
  for RFREE reflections and 1 for the others. The
  number of RFREE reflections is determined by the
  nr_of_rfree argument. By default RFREE
  reflections are selected at random.

  If the optional SHELL keyword is given then RFREE
  reflections will be taken in resolution shells
  The width of the resolution shells is 1/400th of
  the resolution range unless specified otherwise
  by the user. You may wish to try this if you have
  non-crystallographic symmetry. However, to get a
  reasonable number of shells they have to be
  thinner then I like. In the future I may allow to
  actually input your NCS symmetry

SELECT

  OPTION: SELECT [MODE] TARGET CRITERIUM
  ======================================

  Command to select a subset of reflections
  MODE may be one of the following words
   PLUS    : Add selected records to the set
   MINUS   : Remove selected records from the set
   ONLY    : Only selected records will be kept
   NOT     : Invert the selection criterium
             (NOT can combine with other modes)
  CRITERIUM is one the following:
   = val   : select records with target = val
   > val   : select records with target > val
   < val   : select records with target < val
   >= val  : select records with target >= val
   <= val  : select records with target <= val
   <> val  : select records with target <> val
             NOTE: "val" should be either a number
                   or a column reference, e.g. col 1
   ZONE z  : Only when target is INDEX !!! Selects
             indices in zone z, where z is e.g.
             2n or 3n or 2n + 1 etc
   PRESENT : > -1.0E+10 < 1.0E+10
   ABSENT  : NOT PRESENT
   ALL     : select all records, no target needed
   NONE    : deselect all records, no target needed
   INVERT  : select unselected records & vice versa
   SYSABS  : select records with an illegal hkl
   CENTRO  : select centrosymmetric reflections
   ASUERR  : select reflections outside as. unit
   PHAERR  : select centrosymmetric reflections
               with an illegal phase
   MULTI n : select records with multiplicity of n

  TARGET is one of the following:
  COLUMN c1  Keyword followed by column-id
             Criterium refers to column c1
  RESOL      Criterium refers to the resolution
  INDEX idx  Keyword followed by index-code
             index-code is [[+|-]H][[+|-]K][[+|-]L]

  EXAMPLES:
  ========

  In the next examples CURRENT SELECTION is the
  selection from some previous SELECT command

  MODES: ONLY, PLUS, MINUS, NOT
  =============================
  SELECT col 2 > 0
    current selection AND this selection. So the
    AND operator is the default. E.g. you get a
    subset of the current selection
  SELECT only col 2 > 0
    select refs that match this criterium
    independent of the current selection
  SELECT plus col 2 > 0
    current selection OR this selection
  SELECT minus col 2 > 0
    current selection AND NOT this selection
  SELECT not col 2 > 0
    current selection AND NOT this selection
  SELECT plus not col 2 > 0
    current selection or not this selection


  TARGETS: COLUMN, RESOL, INDEX
  =============================
  SELECT column 2 > 0 < 100
    select if value in column 2 is > 2 and < 100
  SELECT column 1 > column 2
    select if value in column 2 is > in column 1
  SELECT resol < 8
    select if resolution is better then 8 A
  SELECT INDEX h = 0
    select the 0kl plane
  SELECT INDEX h - k = 0
    select the hhl plane
  SELECT INDEX h + k + l zone 2n + 1
    select reflections with h+k+l is odd
  SELECT index h = 0
  SELECT index k = 0
  SELECT index l zone 2n +1
    select 00l reflections with l is odd

  CRITERIUM
  =========
  SELECT col 1 = present
    select reflection if column 1 is not MNF
  SELECT col 1 = absent
    select reflection if column 1 is an MNF
  SELECT all
    select all reflections
  SELECT none
    deselect all reflections
  SELECT invert
    invert the selection currently in memory
  SELECT sysabs
    select reflections with indices that should be
    systematically absent (e.g. hkl = 0 3 0 in P2sub1)
  SELECT centro
    select centrosymmetric reflections
  SELECT asuerr
    select reflections outside the asymmetric unit
  SELECT phaerr
    select centrosymmetric reflections with illegal
    phase
  SELECT multi n
    select reflections on a n-fold symmetry axis
    (n must be an integer)

SET

  OPTION: SET ITEMS
  =================

  Command to set header information
  -ITEMS is a list of header items to be changed
   ALL = all header items,
   TITLE = title cards,
   LABELS = column labels,
   TYPES = column types,
   CELL = unit cell parameters,
   SORT = sort order,
   SPACEGROUP = space group related data

  The program will list the old header information.
  The information given by the user will be used to
  replace the old data. If the user just gives a
  return, the old data will be kept.

  For the LABELS and TYPES keywords it is possible
  to modify a single column by giving the column
  ID for that column

  Examples:
  SET CELL
  SET TYPES
  SET TYPES COL 5

SORT

  OPTION: SORT CRITERIUM DIRECTION
  ================================

  Command to sort the structure factor data base.

  CRITERIUM can be one of the following
  -[h k l] sort order may be specified as h k l
   or 1 2 3 or permutations thereof. The default
   is to sort on the current sort order as defined
   in the header info. The indices are always
   sorted in ascending order
  -RESOLution  Sort on resolution
  -COLumn      Sort on content of column id

  DIRECTION can be either:
  -UP    Ascending sort order (this is the default)
  -DOWN  Descending sort order

  Missing data is treated internally as a very
  small number (-1E+10) and will be sorted as such

  WARNING, the RESOL and COL options will mess up
  the index sort order. It is advised to restore
  the old sort order by another call to SORT to
  prevent funny behavior of subsequent options or
  programs :-)

  EXAMPLE: SORT l k h
           SORT resol
           SORT resol down
           SORT col fobs

STOP

OPTION: STOP
============

Terminate the program

WINDOW


  Notice: This option is still in construction. Use it with care!

  OPTION: WINDOW NWIN COL col_id 
  ===============================

  This option creates a new column in which it
  stores a local average of column col_id as
  function of resolution. The average is calculated
  by sorting the reflections by resolution and then
  sliding a window of NWIN reflections along all
  data points in column col_id. The central point
  in the window is set to the average value. For
  the first and last NWIN/2 reflections, which are
  never in the center of the window, the average
  will be obtained by linear extrapolation

WRITE

 OPTION: WRITE FILENAME [FORMAT] [COLUMN columns] [HEADER]
 =========================================================

 Command to write a structure factor file.

 -FILENAME is the name of the file. The program
  will try to deduce the file format from the
  extension. It will recognize .mtz, .mdf, .snd,
  .xpl, .tnt, .31, .fin, .phs and .df
 FORMAT can be one of the following:
  MTZ, MDF, SND, XPL, TNT, 31, FIN, PHS or DF
  or a valid FORTRAN format string (see below).
  This overrules the file name extension format
 COLUMN Keyword to select specific columns.
  Columns can be specified by numbers or labels
  (also mixed), and in any order. The order of
  columns in the output file will reflect the
  specified order and not the order in SFTOOLS
  A column may also be given, and therefore
  written, twice (not always allowed, e.g. MTZ)
  If no columns are given, then the program will
  ask the user for each column whether or not to
  include it. If no COLUMN keyword is given all
  columns are read.
  THE COLUMN KEYWORD MUST BE THE LAST ARGUMENT !

 HEADER Keyword to specify that only the header
        should be written to the given file

 File formats are:
 MTZ   CCP4 format
 MDF   old BIOMOL format
 SND   BIOMOL ascii format
 XPL   XPLOR format
 TNT   TNT format
 31    PHASES long and short binary formats
 FIN   Xtalview fin-format
 PHS   Xtalview phs-format
 DF    Xtalview double fin-format

 NOTE: several file formats do not allow absent
  data. If one or more written columns of a
  reflection contain absent data then the whole
  reflection is rejected

 NOTE: For .fin and .df files sigma and amplitude
  columns are set to 9999 and 0 respectively if
  the sigma column is 0 or either column contains
  absent data

 NOTE: TNT files can have the following columns
  in the given order:
  Fobs, Sigma
  Fobs, Sigma, Phase, FOM
  Fobs, Sigma, Rfree
  Fobs, Sigma, Rfree, Phase, FOM
  Rfree, if present, MUST be column three.

 NOTE: Only the following columns make sense for
  XPLOR: FOBS, SIGMA, FOM, PHASE, WEIGHT, TEST
         FCALC, FPARTIAL, PA, PB, PC and PD.
  Make sure you write out at most one of each type.
  Use the COLUMN option to prevent the output of
  non-sensible columns. If the first 3 characters
  of a column label match the first 3 characters
  of FOBS, SIGMA, FOM, PHASE, WEIGHT, TEST, FCALC,
  FPARTIAL, PA, PB, PC or PD then SFTOOLS assumes
  that that is the XPLOR column type. If your
  column label does not match any of these, SFTOOLS
  will ask you to specify the XPLOR column type

 If you provide a Fortran FORMAT string then the
 first three values MUST be written as integers
 since these are the indices. ALL!!! other values
 MUST!!! be written as reals because that is how
 they are stored inside the program

 Examples:
 WRITE myfile.mtz COLUMN 1 2
 (write column 1 and 2 to myfile.mtz as MTZ file)
 WRITE myfile.hkl MTZ COL 2 1
 (write mtz with column 1 and 2 in reversed order)
 WRITE myfile.hkl FORMAT('HKL ',3i5,2f8.3)
 (write four columns in given format)

MTZ column types

Allowed are the following types :

H = index h, k or l   P = phase angle
J = intensity         F = amplitude
D = anom. diff.       Q = standard deviation
W = weight factor     B = batch number
I = any integer       R = any real
A = phase prob. coeff. (Hendrickson/Lattman)
Y = M/ISYM, partial/reject flag and sym. number

Notes

Memory requirements are governed by parameters set in the sftools.ini file, and these may need to be increased for large problems. The program will inform you if your problem exceeds the current limits. If the program aborts before any program output is displayed (you may see a message "killed") then the array sizes are set too large to be handled by your computer. You must either decrease the array sizes, free up or buy more memory, or increase your swap file.

Program updates in between CCP4 releases will be made available by the author. Please subscribe to the SFTOOLS users list (by sending me an e-mail) or subscribe to the CCP4 bulletin board to be notified of changes.

History

SFTOOLS was created during 1993 at the university of Groningen while converting the BIOMOL software package to the MTZ standard. During the period 1994 till 1998 development was continued a the University of Alberta. In 1998 SFTOOLS was integrated into the CCP4 program package.

REFERENCES

B. Hazes, unpublished results

AUTHOR

Program written by Bart Hazes.

bart.hazes@ualberta.ca

bart@mrc-lmb.cam.ac.uk