Program : CRAVE
Version : 960415
Author : Gerard J. Kleywegt & T. Alwyn Jones,
Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : auto-generate C-shell script for multiple-crystal averaging
of electron-density maps
Package : RAVE
Reference(s) for this program:
* 1 * T.A. Jones (1992). A, yaap, asap, @#*? A set of averaging programs. In "Molecular Replacement", edited by E.J. Dodson, S. Gover and W. Wolf. SERC Daresbury Laboratory, Warrington, pp. 91-105.
* 2 * G.J. Kleywegt & T.A. Jones (1994). Halloween ... Masks and Bones. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 59-66.
* 3 * G.J. Kleywegt & R.J. Read (1997). Not your average density. Structure 5, 1557-1569. [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9438862&form=6&db=m&Dopt=r]
* 4 * G.J. Kleywegt & T.A. Jones (2037 ?). Convenient single and multiple crystal real-space averaging. To be published ???
* 5 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
960409 - 0.01 - first version
960410 - 0.02 - minor changes
960415 - 0.03 - minor bug fixes
Since writing C-shell scripts for doing multiple-crystal form averaging with RAVE can be an accountant's nightmare, this little jiffy will auto-generate such a script from a simple input file.
The input file defines the path names of executables, some file names and a few other things. The output will be a complete C-shell script for executing N cycles of averaging over M crystal forms (1 < M < 26, at present; single-domain averaging only), each with or without NCS.
An example of such an input file is shown below. Cut it out and edit it to suit your needs. Then run CRAVE (takes about a second of CPU time), and execute the resulting script.
Comment lines start with an exclamation mark in column 1; all other lines contain a keyword (4 characters, sometimes including a trailing space), 1 space, and then the value(s).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! ! input file to generate C-shell script for RAVE ! to do multiple crystal averaging ! (sorry, only single domain at present) ! ! format for all lines: KEYWORD (4 characters), 1 space, VALUE ! ! gj kleywegt @ 960409 ! ! usage: run crave < jiffy.inp ! then: chmod +x output_file ! then execute the output_file ! to get a log file, use: output_file |& tee rave.log ! ! commands to invoke various programs: SFAL sfall RSTA rstats FFT /public/src/ccp4_2.13/bin/fft MAVE run mave COMA run comap MAPM run mapman ! ! your work directory WORK /nfs/scr_uu5/gerard/testmave ! identifier IDEN lipase ! number of cycles CYCL 10 ! scratch directory SCRA /nfs/scr_uu1/gerard/scratch/ ! mask in reference crystal MASK p21_new.mask ! ! data for crystal form 1 (reference) ! ! identifier COPY p21 ! mtz file MTZ p21.mtz ! input unit cell map MAP p21_start.E ! mtz file labels for f and sigf LABF F SIGF SIGF ! fft grid and extent GRID 70 48 88 EXTE 0 69 0 47 0 87 ! resolution RESO 8.0 3.0 ! O symm-op file OSYM p21.sym ! all ncs operators NCSO rt_unit.o NCSO p21_a_to_b.o ! cross-crystal operator (= unit oper for form 1) XXRT rt_unit.o ! ! data for crystal form 2 (target) ! COPY p212121 MTZ p212121.mtz MAP p212121_start.E LABF F SIGF SIGF GRID 60 48 90 EXTE 0 59 0 47 0 89 RESO 8.0 3.0 OSYM p212121.sym NCSO rt_unit.o XXRT p21_to_p212121.o ! ! output C-shell script FILE lipase_rave.csh ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
NOTES:
- the RESOlution should be identical for all crystal forms
- the reflections in the input MTZ files *MUST* have been put on
the same temperature factor scale prior to cross-crystal averaging
(see the DATAMAN manual on how to do this) !!!
- OSYM symmetry-operator files are O-style
- NCSO and XXRT operators are based on Cartesian coordinates; use
program IMP to improve NCS operators and the Improve option of
program MAVE to improve cross-crystal operators prior to averaging;
they are in O style
- all FFTs are done in spacegroup P1 for simplicity, so make sure
that the input (unaveraged) maps cover a complete unit cell
- the IDEN and COPY names are used to generate map and log-file names
The program shows what it is doing:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix> run crave < crave.inp...
Max nr of crystal forms : ( 25) Max nr of NCS-ops per form : ( 100) Main keywords : ( SFAL RSTA FFT MAVE COMA FILE MAPM WORK IDEN CYCL SCRA MASK) Form keywords : ( COPY MTZ MAP LABF SIGF GRID EXTE RESO OSYM XXRT NCSO) Crystal form : ( 1) Crystal form : ( 2)
SFAL > (sfall) RSTA > (rstats) FFT > (/public/src/ccp4_2.13/bin/fft) MAVE > (run mave) COMA > (run comap) FILE > (lipase_rave.csh) MAPM > (run mapman) WORK > (/nfs/scr_uu5/gerard/testmave) IDEN > (lipase) CYCL > (10) SCRA > (/nfs/scr_uu1/gerard/scratch/) MASK > (p21_new.mask)
COPY > (p21) MTZ > (p21.mtz) MAP > (p21_start.E) LABF > (F) SIGF > (SIGF) GRID > (70 48 88) EXTE > (0 69 0 47 0 87) RESO > (8.0 3.0) OSYM > (p21.sym) XXRT > (rt_unit.o) NCSO > (rt_unit.o) NCSO > (p21_a_to_b.o)
COPY > (p212121) MTZ > (p212121.mtz) MAP > (p212121_start.E) LABF > (F) SIGF > (SIGF) GRID > (60 48 90) EXTE > (0 59 0 47 0 89) RESO > (8.0 3.0) OSYM > (p212121.sym) XXRT > (p21_to_p212121.o) NCSO > (rt_unit.o)
Nr of crystal forms : ( 2) Nr of averaging cycles : ( 10)
TASK > (CYCLE lipase 0) TASK > (average p21 0) TASK > (average p212121 0) TASK > (comap lipase 0)
TASK > (CYCLE lipase 1) TASK > (expand p21 1) TASK > (expand p212121 1) TASK > (sfall p21 1) TASK > (rstats p21 1) TASK > (fft p21 1) TASK > (average p21 1) TASK > (sfall p212121 1) TASK > (rstats p212121 1) TASK > (fft p212121 1) TASK > (average p212121 1) TASK > (comap lipase 1)
TASK > (CYCLE lipase 2)
...
TASK > (comap lipase 10)
TASK > (mapman lipase 10) TASK > (all done lipase 10)
*** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE ***
Version - 960410/0.02 Started - Wed Apr 10 19:38:43 1996 Stopped - Wed Apr 10 19:38:44 1996
CPU-time taken : User - 1.3 Sys - 0.1 Total - 1.4
*** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE ***
>>> This program (C) 1993-96, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE *** CRAVE *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The example above produces a script for ten cycles of averaging over two crystal forms, one in P21 with two-fold NCS, and one in P212121 without NCS:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- #!/bin/csh -f # Created by CRAVE V. 960410/0.02 at Wed Apr 10 19:38:43 1996 for user gerardcd /nfs/scr_uu5/gerard/testmave
echo echo CYCLE lipase 0 echo if (! -e p21_new.mask ) then echo ERROR ... file p21_new.mask not found ... aborting exit -1 endif if (! -e p21_start.E ) then echo ERROR ... file p21_start.E not found ... aborting exit -1 endif if (! -e rt_unit.o ) then echo ERROR ... file rt_unit.o not found ... aborting exit -1 endif if (! -e p21.sym ) then echo ERROR ... file p21.sym not found ... aborting exit -1 endif if (! -e rt_unit.o ) then echo ERROR ... file rt_unit.o not found ... aborting exit -1 endif if (! -e p21_a_to_b.o ) then echo ERROR ... file p21_a_to_b.o not found ... aborting exit -1 endif echo echo average p21 0 echo run mave -b << EOF >& p21_average_0.log average p21_start.E p21_new.mask rt_unit.o p21.sym rt_unit.o p21_a_to_b.o
p21_start.E /nfs/scr_uu1/gerard/scratch/p21_0x.E EOF
if (! -e /nfs/scr_uu1/gerard/scratch/p21_0x.E ) then echo ERROR ... file /nfs/scr_uu1/gerard/scratch/p21_0x.E not found ... aborting exit -1 endif grep -i "error" p21_average_0.log grep -i "Corr. coeff. for operator" p21_average_0.log grep -i "R-factor for operator" p21_average_0.log
...
if (! -e /nfs/scr_uu1/gerard/scratch/lipase_10.E ) then echo ERROR ... file /nfs/scr_uu1/gerard/scratch/lipase_10.E not found ... aborting exit -1 endif grep -i "error" lipase_comap_10.log grep -i "Corr coeff :" lipase_comap_10.log echo echo mapman lipase 10 echo run mapman -b << EOF >& lipase_mapman_10.log read m1 /nfs/scr_uu1/gerard/scratch/lipase_10.E ccp4 mappage m1 final.omap EOF
if (! -e final.omap ) then echo ERROR ... file final.omap not found ... aborting exit -1 endif echo echo all done lipase 10 echo exit 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
To run the script, do something like:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix> chmod +x lipase_rave.csh unix> nohup lipase_rave.csh |& tee lipase.log & ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When executed, the script takes about 20 CPU minutes on a DEC/Alpha (in fact, 6 cycles would have been enough). The R-factors (Fo,Fc) start at > 40% and come down to ~18%; the correlation of the density in the two crystal forms goes up from ~0.55 to > 0.85.
The final averaged map will always be called final.omap in your work directory; you can contour it in O immediately (the intermediate CCP4 maps will be in your scratch directory).
None, at present.
Created at Fri Dec 18 19:42:07 1998
by MAN2HTML version 971024/1.6