ABS (CCP4: Supported Program)

NAME

   abs - A program to determine the absolute configuration (hand) of
   the heavy atom substructure and calculate a FOM.

SYNOPSIS

   abs hklin foo_in.mtz
   [Key-worded input]

DESCRIPTION

   ABS is a program to determine the absolute configuration (hand) of
   the heavy atom substructure or polar space group using anomalous
   scattering. It also calculates a figure of merit which is a useful
   assessment of the heavy atom substructure. The algorithm is based
   on the Ps function method (Woolfson & Yao, 1994 and Hao & Woolfson,
   1989).

   The program can be used as soon as anomalous sites are determined,
   although the result may be more clear-cut after refinement of the
   sites.

INPUT AND OUTPUT FILES

  Input

   HKLIN
          (compulsory)
          Input MTZ file. This should contain the conventional (CCP4)
          asymmetric unit of data (preferably from TRUNCATE). See the
          LABIN keyword for columns used.

  Output

          Results are shown in the log file.

KEYWORDED INPUT

   The various data control lines are identified by keywords. Only the
   first 4 characters of a keyword are significant. The cards can be
   in any order. Numbers in [ ] are optional and can be left out. The
   available keywords are:

     TITLE, LABIN, RESOLUTION, ATOM

  TITLE <title string>

   Upto 80 character title.

  LABIN F=...  SIGF=...  DANO=...  SIGDANO=...

   (Compulsory.)
   F: mean F magnitude.
   SIGF: standard deviation of F.
   DANO: Friedel difference. Must be column type D.
   SIGDANO: standard deviation of F2.

  RESOLUTION <rmin>

   High resolution cutoff in Angstrom (default value = 4).

  ATOM <x> <y> <z> [<occupancy>]

   (compulsory)
   Fractional coordinates of anomalous scatterer(s).


PRINTER OUTPUT

   The value of C (the normalised value of C3, see reference below) is
   printed out. If this is positive, then the input atom configuration
   is likely correct. If it is negative, then it is likely incorrect.

   The  absolute  value of C gives an indication of how well the
   substructure  has  been determined. C < 0.01 indicates a poor
   substructure solution, while C > 0.02 indicates a good substructure
   solution.

   The    program    also    outputs    a    figure   of   merit
   <|sin(phase_ha_substructure)|>

EXAMPLES

  Unix example script found in $CEXAM/unix/runnable/

     * abs.exam

  Non-runnable examples

abs hklin /ccpdisk/xtal/ccp4/new_programs_4.2/hao_/ompdc.mtz <<eof
TITLE determination of absolute configuration
RESO 3.0
ATOM   0.88364   0.45255   0.20904
ATOM   0.78647   0.72103   0.20167
ATOM   0.84051   0.61635   0.11817
ATOM   0.72479   0.61860   0.11258
ATOM   0.72077   0.55255   0.14145
ATOM   0.59536   0.59265   0.24685
ATOM   0.86602   0.58829   0.40655
ATOM   0.77843   0.69468   0.11515
ATOM   0.75302   0.81095   0.19786
ATOM   0.69114   0.73137   0.22579
ATOM   0.61948   0.76388   0.20633
ATOM   0.54273   0.63876   0.12769
ATOM   0.63899   0.79544  -0.08076
ATOM   0.48613   0.55253   0.55323
ATOM   0.61479   0.44768   0.54001
ATOM   0.55872   0.43179   0.61568
ATOM   0.62674   0.45720   0.64670
ATOM   0.53478   0.56807   0.73165
ATOM   0.66755   0.78155   0.57921
LABIN F=F2 SIGF=SIGF2 DANO=DANO2 SIGDANO=SIGDANO2
eof

REFERENCES

    1. Hao, Q. (2004) J. Appl. Cryst. 37, 498-499. ABS: a program to
       determine  absolute  configuration and evaluate anomalous
       scatterer substructure.

AUTHORS

   Q. Hao

   MacCHESS, Wilson Synchrotron Lab, Cornell University, NY 14850, USA

   Email: qh22@cornell.edu