XDLDATAMAN (CCP4: Supported Program)

NAME

SYNOPSIS

DESCRIPTION

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.

HISTORY

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 OPTIONS

READ A DATASET

LIST DATASET INFORMATION

STATISTICS OF THE DATASET

EFFECTIVE RESOLUTION

RSYM HKL/KHL REFLECTIONS

CELL CONSTANTS

SYMMETRY OPERATORS

CALCULATE/DEDUCE/CONVERT

RESOLUTION

Calculate the resolution of all reflections.

CENTRICS/ACENTRICS

Assign centric/acentric flag to each reflection.

ORBITAL MULTIPLICITY

Calculate the orbital multiplicity of each reflection.

F -> I CONVERSION

Convert Fs to Is by using: I ~ F*F.

I -> F CONVERSION

Convert Is to Fs by using: F ~ sqrt(I) (I>=0).

TYPE SOME REFLECTIONS

SHOW SOME REFLECTIONS

FOBS >

Provide a number; all reflections with F greater than this number will be listed.

FOBS <

Provide a number; all reflections with F smaller than this number will be listed.

SIGMA >

Provide a number; all reflections with sigma(F) greater than this number will be listed.

SIGMA <

Provide a number; all reflections with sigma(F) smaller than this number will be listed.

F/SIGMA >

Provide a number; all reflections with F/sigma(F) greater than this number will be listed.

F/SIGMA <

Provide a number; all reflections with F/sigma(F) smaller than this number will be listed.

RESOLUTION >

Provide a number; all reflections with a resolution greater than this number will be listed (note: greater means "lower resolution" !).

RESOLUTION <

Provide a number; all reflections with a resolution smaller than this number will be listed (note: smaller means "higher resolution" !).

SPECIAL REFLECTIONS

ABSENCES LIST

TWIN STATISTICS

GEMINI TWIN ANALYSIS

TEMPERATURE FACTOR APPLY

CHANGE INDEX

PROD/PLUS

FOBS

Provide two numbers X and Y; all Fs will be replaced by X*F+Y.

SIGMA(FOBS)

Provide two numbers X and Y; all sigmas will be replaced by X*sigma+Y.

BOTH

Provide two numbers X and Y; all Fs and sigmas will be replaced by X*F+Y and X*sigma+Y, respectively.

LAUE GROUP APPLY

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 REFLECTIONS

KILL SOME REFLECTIONS

FOBS >

Provide a number; all reflections with F greater than this number will be deleted.

FOBS <

Provide a number; all reflections with F smaller than this number will be deleted.

SIGMA >

Provide a number; all reflections with sigma(F) greater than this number will be deleted.

SIGMA <

Provide a number; all reflections with sigma(F) smaller than this number will be deleted.

F/SIGMA >

Provide a number; all reflections with F/sigma(F) greater than this number will be deleted.

F/SIGMA <

Provide a number; all reflections with F/sigma(F) smaller than this number will be deleted.

RESOLUTION >

Provide a number; all reflections with a resolution greater than this number will be deleted (note: greater means "lower resolution" !).

RESOLUTION <

Provide a number; all reflections with a resolution smaller than this number will be deleted (note: smaller means "higher resolution" !).

ERASE OPTIONS

ROGUES

Delete "rogue" reflections simply by providing their HKL indices. This can be used to remove individual reflections which are suspect for some reason or other.

ODD H/K/L

Delete all reflections for which either H, K or L is odd.

EVEN H/K/L

Delete all reflections for which either H, K or L is even.

RFREE OPTIONS

INITIALISE

Set the seed for the random-number generator. Providing a negative seed will use the current machine clock value as the seed; a positive number will be used itself as the seed.

LIST CURRENT STATUS

This lists the current partitioning of the dataset in WORK and TEST reflections. If there are very few or very many TEST reflections, a warning message will be printed. In general, 10% of the data with a minimum of ~500 and a maximum of ~2000 TEST reflections is considered to be reasonable. Note that the error in Rfree is roughly equal to 1/SQRT(number of TEST reflections), so that for 500 TEST reflections the error is ~4.5% and for 2000 TEST reflections ~2.2%.

RESET ALL RFREE FLAGS

This sets all Rfree flags to zero, i.e. all reflections are flagged as WORK reflections. See RFREE FLAGS.

GENERATE RANDOM RFREE FLAGS

Provide either the *percentage* or (roughly) the *number* of TEST reflections. Randomly chosen reflections will be assigned as TEST reflections (the same way X-PLOR does this). This is actually the worst possible way to select TEST reflections, since (through the G-function) every reflection will be related to its neighbours (in reciprocal space) and, in the case of NCS, to its "NCS mates" and their neighbours.

SHELLS OF RFREE REFLECTIONS

Provide the *percentage* or (roughly) the *number* of TEST reflections and the number of resolution bins. The data will be sorted by resolution and divided into bins. From every bins the appropriate fraction of reflections from its centre will be flagged as being TEST reflections. This is to counter couplings in the case of NCS.

SPHERES OF RFREE REFLECTIONS

Provide the *percentage* or (roughly) the *number* of TEST reflections and the radius of reciprocal-space spheres. Reflections are picked at random, and they and their neighbours inside a small sphere (in reciprocal space) are all assigned as TEST reflections. This is to counter couplings due to bulk solvent in the absence of NCS.

GSHELDRICKS METHOD

This simply assigns every N-th reflection to be a TEST reflection, where the value of N is provided by the user (in SHELX, N=10).

COMPLETE CROSS-VALIDATION SETS

The number N of datasets to be generated is provided. Every reflection will be assigned to be a TEST reflection in exactly one of the N datasets. The N datasets are written in X-PLOR format (but can, of course, be converted into other formats with this program).

WRITE DATASET TO FILE

DELETE CURRENT DATASET

HELP

QUIT

FORMATS

* (free format)

MTZDUMP (user or free format)

XPLOR (no format required)

SHELXS (fixed format)

TNT (free format)

PROTEIN (user or free format)

MKLCF (user or free format)

HKLFS (user or free format)

RFREE (user or free format)

ELEANOR (user or free format)

Supported output formats :

* (fixed format)

RXPLOR (no format required)

SHELXS (fixed format)

TNT (fixed format)

PROTEIN (user or fixed format)

CIF (user or fixed format)

MKLCF (user or fixed format)

HKLFS (user or fixed format)

RFREE (user or fixed format)

ELEANOR (user or fixed format)

XPLOR (no format required)

Notes on formats :

*/HKLFS - reads/writes HKL F Sigma

RXPLOR - X-PLOR format with Rfree flags

SHELXS - fixed format, no Rfree flags

TNT - no FOMs, phases or Rfree flags

PROTEIN - no Sigmas

MKLCF - integer F and Sigma

RFREE - HKL F Sigma and integer Rfree flags

ELEANOR - ditto, but real (1.0-Rfree) flags

MTZDUMP - reads unedited MTZDUMP log file

CIF - output only; Rfree flags UNofficial

Use the Calculate option to convert I<->F if needed.

RFREE FLAGS

REFERENCES

1. XDLDATAMAN:
   G.J. Kleywegt & T.A. Jones (1996), Acta Cryst. D52, 826-828.
2. XDL_VIEW:
   J.W. Campbell (1995). "XDL_VIEW, an X-windows-based toolkit for crystallographic and other applications", J. Appl. Cryst. 28, 236-242.
3. RAVE:
   G.J. Kleywegt & T.A. Jones (1994). "Halloween ... Masks and Bones", in "From First Map to Final Model" (S. Bailey, R. Hubbard & D. Waller, Eds.), SERC Daresbury Laboratory, pp. 59-66.
4. O:
   T.A. Jones, J.Y. Zou, S.W. Cowan, & M. Kjeldgaard (1991). "Improved methods for building protein models in electron density maps and the location of errors in these models", Acta Cryst. A47, 110-119.
5. GEMINI:
   E. Stanley (1972). "The identification of twins from intensity statistics", J. Appl. Cryst. 5, 191-194.
6. GEMINI:
   D.C. Rees (1980). "The influence of twinning by merohedry on intensity statistics", Acta Cryst. A36, 578-581.
7. RFREE:
   A.T. Brunger (1992). "Free R value: a novel statistical quantity for assessing the accuracy of crystal structures", Nature 355, 472-475.
8. CCP4:
   Collaborative Computational Project Number 4 (1994). "The CCP4 suite: programs for protein crystallography", Acta Cryst. D50, 760-763.

KNOWN BUGS

AUTHORS

SEE ALSO