FSEARCH (CCP4: Supported Program)
fsearch - A program to perform up to 6 dimensional molecular
(envelope) replacement search.
fsearch hklin foo_in.mtz [flmin foo_in.txt]
[xyzinfoo_in.pdb] [mapin foo_in.map]
FSEARCH can be used for a molecular-replacement (up to 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 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
(Envelope input mode; ONLY one from the following three)
Spherical Harmonics File. Free format: L M Flm(re) Flm(im).
Coordinates File (Brookhaven format).
Map File - one asymmetric unit only (standard CCP4 map file format).
Results (up to 200 solutions sorted by R-factor) are shown in the log
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>
Up to 80 character title.
LABIN FP=... SIGFP=...
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).
High resolution cutoff in Angstrom (default value = 10).
Reflections will be excluded if F < Nsig*SIGF. Default: no reflections
Solutions with R-factor < rf will be written to the log file. Default:
rf = 0.60.
= 1 orthogonal x y z along a, c*xa, c*
= 2 b, a*xb, a*
= 3 c, b*xc, b*
= 4 a+b, c*x(a+b), c*
= 5 a*, cxa*, c (Rollett)
Check packing clashes (% of the whole unit cell). Note: this can be *very
time consuming*, therefore not recommended for the initial search. Default:
ALPHA <min> <max> <step>
Search range and step on Eulerian angle alpha (in degrees). Default: 0
BETA <min> <max> <step>
Search range and step on Eulerian angle beta (in degrees). Default: 0
GAMMA <min> <max> <step>
Search range and step on Eulerian angle gamma (in degrees). Default: 0
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.
Results (up to 200 solutions sorted by R-factor) are shown in the log file.
Unix examples script found in $CEXAM/unix/runnable/
Non-runnable example script
fsearch hklin pfsodb.mtz xyzin sod3.pdb <<eof
# 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
Code for an MPI-parallelised version of FSEARCH is distributed as
fsearch_mpi.f This is not integrated into the CCP4 installation,
and needs to be built separately. You will need:
The program distributes the search over Eulerian angles alpha and beta
over the available processors (with one processor reserved as a master
node). By default, 3 processors are used for the beta search for each
trial alpha angle. The search over alpha is then split over how ever many
sets of 3 processors there are. If the total number of processors (not
including the master node) is not a multiple of 3, then the last 1 or 2
processors are not used. The number of processors for the beta search
can be changed from the default value of 3 by the keyword PBET (e.g. "PBET 5").
- An MPI compiler, such as
MPICH or LAM.
- The link line will need to include to the MPI library as well as the
usual CCP4 libraries (possible names libmpich.a, libmpif.a, libfmpi.a)
- The source code fsearch_mpi.f includes the system file "mpif.h". This may
need to be adjusted.
- Hao, Q. (2001), Acta Cryst. D57 1410-1414. "Phasing from an Envelope".
- Q. Liu, A. J. Weaver, T. Xiang, D. J. Thiel and Q. Hao,
(2003) Acta Cryst. D59 1016-1019.
"Low-resolution molecular replacement using a six-dimensional search"
Quan Hao, Cornell University.