FSEARCH (CCP4: Supported Program)
NAME
fsearch - A program to perform upto 6 dimensional molecular
(envelope) replacement search.
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, LABIN,
GRID, RESOLUTION,
SIGCUT, RFILTER,
ORTH, CHKOVERLAP,
ALPHA, BETA,
GAMMA, XRANGE,
YRANGE, ZRANGE
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.
GAMMA <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
Non-runnable example script
fsearch hklin pfsodb.mtz xyzin sod3.pdb <<eof
TITL SOD
# GRID 48 52 150
LABI FP=FP SIGFP=SIGFP
ALPHA 0 0 1
BETA 0 0 1
GAMMA 0 30 3
XRANGE 0 18 3
YRANGE 0 25 1
ZRANGE 0 58 1
RESO 6
eof
REFERENCES
Hao, Q. (2001), Acta Cryst. D57. 1410-1414. "Phasing from an Envelope".
AUTHOR
Quan Hao, Cornell University.
Email: qh22@cornell.edu.