FSEARCH (CCP4: Supported Program)

NAME

fsearch -  A program to perform upto 6 dimensional molecular (envelope) replacement search.

Source Code

fsearch.f (SHIFT click to save on disk)
To compile: f77 -o fsearch fsearch.f -L$CCP4_LIB -lccp4
On a Linux box, use: f77 -o fsearch -static -fno-second-underscore -fno-globals fsearch.f -L$CCP4_LIB -lccp4

SYNOPSIS

fsearch hklin foo_in.mtz [flmin foo_in.txt] [xyzinfoo_in.pdb] [mapin foo_in.map]
[Key-worded input]

DESCRIPTION

FSEARCH can be used for a molecular-replacement (upto 6 dimensional) solution  given a predetermined envelope from any source, provided that the envelope can be converted to the standard CCP4 map format or expressed in terms of spherical harmonics or generated from a pdb file.

INPUT AND OUTPUT FILES

Input

HKLIN
(compulsary)
Input MTZ file. This should contain the conventional (CCP4) asymmetric unit of data (must be *sorted* on H K L). See the LABIN keyword for columns used.
(Envelope input mode; ONLY one from the following three)
FLMIN
Spherical Harmonics File. Free format: L  M  Flm(re)  Flm(im).
XYZIN
Coordinates File (Brookhaven format).
MAPIN
Map File - one asymmetric unit only (standard CCP4 map file format).

Output

Results (upto 200 solutions sorted by R-factor) 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 only compulsory command is LABIN. The available keywords are:

TITLE <title string>

Upto 80 character title.

LABIN FP=...  SIGFP=...

(Compulsory.)
E.g.
FP=F  SIGFP=SIGF.

GRID <nx> <ny> <nz>

Number of sampling divisions along whole cell edge. For all space-groups, NX,NY,NZ must be even and must have no prime factors greater than 19. Default values: nx = a, ny = b and nz = c (nearest integer in Angstrom).

RESOLUTION <rmin>

High resolution cutoff in Angstrom (default value = 10).
 

SIGCUT <Nsig>

Reflections will be excluded if F < Nsig*SIGF. Default: no reflections are excluded.

RFILTER <rf>

Solutions with R-factor < rf will be written to the log file. Default: rf = 0.60.

ORTH <code>

Orthonormalization code.
      = 1 orthogonal x y z along a,c*xa,c* (Brookhaven, default)
      = 2 b,a*xb,a*
      = 3 c,b*xc,b*
      = 4 a+b,c*x(a+b),c*
      = 5 a*,cxa*,c   (Rollett)

CHKOVERLAP

Check packing clashes (% of the whole unit cell). Note: this can be *very time consuming*, therefore not recommended for the initial search. Default: no checking.

ALPHA <min> <max> <step>

Search range and step on Eulerian angle alpha (in degrees). Default: 0  180  3.

BETA <min> <max> <step>

Search range and step on Eulerian angle beta (in degrees). Default: 0  180  3.

GAMA <min> <max> <step>

Search range and step on Eulerian angle gama (in degrees). Default: 0  180  3.

XRANGE <min> <max> <step>

Search range and step on X (in Angstroms). Default: 0  a/2  1.

YRANGE <min> <max> <step>

Search range and step on Y (in Angstroms). Default: 0  b/2  1.

ZRANGE <min> <max> <step>

Search range and step on Z (in Angstroms). Default: 0  c/2  1.

PRINTER OUTPUT

Results (upto 200 solutions sorted by R-factor) are shown in the log file.
 

EXAMPLES

Unix example script

REFERENCES

Hao, Q. (2001), Acta Cryst. D57. 1410-1414. "Phasing from an Envelope".

AUTHOR

Quan Hao, Cornell University. Email: qh22@cornell.edu.