XDLDATAMAN (CCP4: Supported Program)
NAMExdldataman - X-windows tool; manipulation, analysis and reformatting of reflection files.
SYNOPSISxdldataman [-font1 | font2 | font3 | font4 | font5]
[menu-driven command selection; interactive parameter input]
DESCRIPTIONxdldataman can be used to read, write, analyse and manipulate ASCII reflection files from most biomacromolecular refinement packages packages. No binary reflection file types are supported (i.e.: MTZ files can *not* be read).
The program runs in interactive mode only. It uses the XDL_VIEW toolkit of J.W. Campbell to provide an easy-to-use interface. Commands are selected by clicking on the desired menu option; some menu options give a pop-up sub-menu with further options (indicated by "-->" in the menu name).
File formats are selected with pop-up menus; all other parameters are set in pop-up dialogue boxes (cut-and-paste is supported). In most cases, default values are given in [square brackets]. To accept these defaults, hit the RETURN key. If multiple numbers are to be input (e.g., cell constants), and if only the first one needs to be changed, for instance, typing the new value for this first number followed by the RETURN key will preserve the values for the other five numbers.
There is a command line option (-font?) which will determine the size of the menu font. These fonts refer to the xdl fonts which are defined from 1 to 5. This can be useful if the window size is too large for the screen. The default font size is 2. The font definitions can be changed in the .Xdefaults file or xrdb, however all xdl programs will be then be effected.
Output from the program is written to a separate area of the main window. Output can be scrolled and cut and pasted into other documents.
For lengthy operations a progress bar shows how much of the operation has been completed.
HISTORYxdldataman is a CCP4 special version of DATAMAN (part of the Uppsala RAVE averaging package). This version is entirely interactive and has a user-friendly interface. However, this version can only handle one dataset at a time, and some of the functionality of the parent program is absent.
DATAMAN was originally written as a simple format-exchange program, to convert MTZDUMP files to X-PLOR reflection files. It has grown quite a bit since then to include other formats and to carry out several everyday manipulations on datasets. It also includes several programs that were previously stand-alone jiffies (such as the Gemini twin analysis command).
Some of the operations are implementations of Gerard Bricogne's algorithms as described in Volume B of the International Tables.
MENU OPTIONSCommands are issued by moving the pointer over the desired menu option and clicking with the left mouse button.
READ A DATASETProvide the filename and then select the appropriate file type from the pop-up menu. See FORMATS.
LIST DATASET INFORMATIONThis prints some information regarding the dataset that is currently in memory.
STATISTICS OF THE DATASETThis lists the mean, standard deviation, minimum and maximum values of all properties of the dataset that are known.
EFFECTIVE RESOLUTIONThis calculates an estimate of the effective resolution of the dataset, defined as "the resolution at which the actual number of reflections in the current dataset would constitute a 100% complete dataset" (B. Hazes, personal communication). This number is listed for all reflections, and for all reflections with F > n * sigma(F), with n=1,...,5. The lattice type and the number of asymmetric units need to be provided (they are used to estimate the volume of reciprocal space covered by the data).
RSYM HKL/KHL REFLECTIONSThis calculates Rsym (on Fs and on Is, assuming that I=F*F) for all reflection pairs HKL and KHL. If the spacegroup is, for instance, P3x or I4x and this Rsym is low, there may be a spacegroup error (e.g., the spacegroup is P41212 instead of P41).
CELL CONSTANTSEnter the cell constants (needed to calculate the resolution of the reflections).
SYMMETRY OPERATORSProvide the name of a symmetry-operator file in O format.
CALCULATE/DEDUCE/CONVERTThis command has several sub-options:
TYPE SOME REFLECTIONSUse this command to list some reflections. Provide the number of the first and last reflection and the step size (e.g., step size 10 will list every 10-th reflection). Providing a negative number for the last reflection is taken to mean the actual last reflection. Providing a value of zero for the step size will print only the first and the last reflection. Providing a negative step size means "show N reflections equally spread between the first and the last", with N being -1 * the step size.
SHOW SOME REFLECTIONSThis command has several sub-options:
SPECIAL REFLECTIONSList all reflections of a certain type. Provide a template of the type of reflections to be shown (containing the characters H, K, L and/or 0). For example: HHH, 0K0, KK0, etc.
ABSENCES LISTList reflections that are systematically absent according to the current spacegroup symmetry operators. This can sometimes be used to make educated guesses concerning the nature of certain screw axes (e.g., in P4x, if only 00L, with L=4N, are strong reflections x is probably 1 or 3).
TWIN STATISTICSPrint some intensity statistics that may or may not be able to provide information with respect to possible twinning.
GEMINI TWIN ANALYSISThis implements intensity analysis options as described by Stanley (1972) and Rees (1980), that may be of help in investigating possible merohedral twinning. The output consists of statistics and an estimate of the most likely twin fraction ("0.0" means no merohedral twinning). In addition, two PostScript files are produced showing 1N(z,alpha) as a function of z for centro- and non-centrosymmetric reflections. See the original papers for more information.
TEMPERATURE FACTOR APPLYApply a temperature factor to the Fs.
CHANGE INDEXRe-index data. This may be necessary when the data-processing program yields a cell with beta < 90 in a monoclinic spacegroup, or when two datasets cannot be merged due to indexing along equivalent, but different axes (e.g., in P3x, P4x, etc.). Provide expressions for the new H, K and L.
PROD/PLUSThis command has several sub-options:
LAUE GROUP APPLYMove the reflections into the asymmetric unit appropriate for the Laue group of the dataset. This is sometimes necessary when the data-processing program outputs a non-standard asymmetric unit (for instance, R-AXIS processing software in P4x gives an asymmetric unit which is incompatible with the CCP4 standard). The Laue group is selected from a pop-up menu.
Implemented Laue groups and their asymmetric units are:
1bar, hkl:h>=0 0kl:k>=0 00l:l>=0 1bar, hkl:k>=0 h0l:l>=0 h00:h>=0 1bar, hkl:l>=0 hk0:h>=0 0k0:k>=0 2/m, hkl:k>=0, l>=0 hk0:h>=0, k>=0 2/m, hkl:h>=0, l>=0 0kl:k>=0, l>=0 (2-nd sett) mmm, hkl:h>=0, k>=0, l>=0 4/m, hkl:h>=0, k>0, l>=0 with k>=0 for h=0 4/mmm, hkl:h>=0, h>=k>=0, l>=0 3bar, hkl:h>=0, k<0, l>=0 including 00l 3bar, hkl:h>=0, k>0 including 00l:l>0 3barm, hkl:h>=0, k>=0 with k<=h; if h=k l>=0 6/m, hkl:h>=0, k>0, l>=0 with k>=0 for h=0 6/mmm, hkl:h>=0, h>=k>=0, l>=0 m3, hkl:h>=0, k>=0, l>=0 with l>=h, k>=h for l=h, k>h if l>h m3m, hkl:k>=l>=h>=0
SORT REFLECTIONSSort the reflections by their indices H, K and L. The sort order is determined by the user.
KILL SOME REFLECTIONSThis command has the same sub-options as SHOW SOME REFLECTIONS:
ERASE OPTIONSThis command has the several sub-options:
RFREE OPTIONSThis command has the several sub-options:
WRITE DATASET TO FILEProvide the filename and select the desired file type from the pop-up menu.
DELETE CURRENT DATASETRemove the current dataset from memory.
HELPThis prints some brief information. Subsequently, click on *any* menu command to get a brief explanation of what that command does.
QUITStop working with the program.
FORMATSSupported input formats :
Supported output formats :
Notes on formats :
RFREE FLAGSxdldataman uses the X-PLOR convention, i.e. the Rfree flag is an integer number (0 or 1), and a value of "1" means that the reflection belongs to the TEST set which is *not* used in refinement. CCP4 has a different convention: reflections are divided into a number of equal-sized sets, one of which (usually flagged "0") represents the TEST set, see program FREERFLAG. The CCP4 convention is supported (and converted) through the "ELEANOR" format.
KNOWN BUGSNone (at the time of writing).
If you improve the program, please notify GJK of your changes so that they can be implemented in future versions and the entire community may benefit from them (E-mail a brief description and the relevant pieces of code to "email@example.com").
AUTHORSOriginators: G.J. Kleywegt & T.A. Jones, Uppsala
SEE ALSOxdlmapman, mtzdump