!
! pre_oops.omac - gj kleywegt @ 19940308 / 20020730
!
! creates some datablocks needed for oops
! does 3 types of RSFIT, as well as PEPFLIP and RSC
!
$ echo "... pre_oops.omac started at " `date` > q1
!
bell
print ...
# Type "save" if you want to save your database now ... #
!
symbol rsrmap # Which map file ? #
!
symbol mymol # Name of the molecule ? #
!
symbol first # Name of first protein residue ? #
!
symbol last # Name of last protein residue ? #
!
bell print ...
print ... the values of A0 and C depend on
print ... the resolution of your map
print ... res ~ 1.7 - 1.9 - A0 = 0.90 - C = 1.04
print ... res ~ 2.0 - 2.3 - A0 = 0.90 - C = 0.91
print ... res ~ 2.4 ------- A0 = 0.90 - C = 0.82
print ... res ~ 3.2 - 3.5 - A0 = 0.85 - C = 0.55
print ... for other resolutions, optimise the
print ... values of A0 and C (see question Q.030 of the FAQ)
print ...
!
symbol mya0 # Value for A0 ? #
!
symbol myc # Value for C ? #
!
! first write out the molecule and read it in again
! as molecule JUNKY
!
print ... copying $mymol to a temporary molecule JUNKY
sam_atom_out q.pdb $mymol ;;;;;
pdb_read q.pdb junky y n
$ /bin/rm q.pdb
!
! draw a Ca trace and centre on it
!
print ... drawing and centering on JUNKY
mol junky obj junky ca ; end
centre_zone junky $first $last
!
! set parameters for rsfit
!
print ... setting RSFIT parameters
rsr_map $rsrmap
;
!
db_kill .rsr*
db_set_dat .rsr_real 7 7 $myc
db_set_dat .rsr_real 8 8 $mya0
db_set_dat .rsr_real 11 11 1.0
!
! do ALL ATOMS rs-fit
!
print ... RSFIT all atoms
read odat/rsfit_all.o
rs_fit junky $first $last
copy_db junky_residue_all_rsfit junky_residue_rsfit
!
! do MC ATOMS rs-fit
!
print ... RSFIT main chain atoms
read odat/rsfit_mc.o
rs_fit junky $first $last
copy_db junky_residue_mc_rsfit junky_residue_rsfit
!
! do SC ATOMS rs-fit
!
print ... RSFIT side chain atoms
read odat/rsfit_sc.o
rs_fit junky $first $last
copy_db junky_residue_sc_rsfit junky_residue_rsfit
!
! do pep-flip
!
print ... PEPFLIP
pep_flip junky $first $last
!
! do rsc
!
lego_setup
on
;
odat/dgnl.o
odat/dgnl_rna.o
odat/
odat/rsc.o
!
print ... RSC
rsc junky $first $last
!
! print RS-fit statistics
!
print ...
print ... statistics for RSFIT ALL atoms ...
db_stat junky_residue_all_rsfit
print ... statistics for RSFIT MC atoms ...
db_stat junky_residue_mc_rsfit
print ... statistics for RSFIT SC atoms ...
db_stat junky_residue_sc_rsfit
print ... statistics for PEPFLIP ...
db_stat junky_residue_pepflip
print ... statistics for RSC ...
db_stat junky_residue_rsc
!
! write datablocks for OOPS
!
print ...
print ... writing datablocks for OOPS ...
write junky_residue_name resnam.o ;
write junky_residue_type restyp.o ;
!
write junky_residue_all_rsfit rsfit_all.o (10f7.3)
write junky_residue_mc_rsfit rsfit_mc.o (10f7.3)
write junky_residue_sc_rsfit rsfit_sc.o (10f7.3)
!
write junky_residue_pepflip pepflip.o (10f5.3)
write junky_residue_rsc rsc.o (10f5.3)
!
! sometimes O prints "*****" in a PEPFLIP or RSC datablock;
! replace such entries by "9.999"
! NOTE: FIVE times [*] since the format was F5.3 !!!
!
$ sed -e s/[*][*][*][*][*]/9\.999/g pepflip.o > q2
$ sed -e s/[*][*][*][*][*]/9\.999/g rsc.o > q3
$ mv q2 pepflip.o ; mv q3 rsc.o
!
! and now the big trick: the datablocks must have
! the same name as our actual molecule
! this requires some shell programming ...
!
! - write the symbols to a file
!
write .symbols q2 ;
!
! - our real molecule name is symbol MYMOL; extract it
!   and put it in a file (in uppercase)
!
$ grep MYMOL q2 | cut -d" " -f2 | tr '[a-z]' '[A-Z]' > q3
!
! - generate an input file for the stream editor
!
$ echo "s/JUNKY/"`cat q3`"/" > q4
!
! - now change the datablock names
!
$ sed -f q4 resnam.o > q5 ; mv q5 resnam.o
$ sed -f q4 restyp.o > q5 ; mv q5 restyp.o
$ sed -f q4 rsfit_all.o > q5 ; mv q5 rsfit_all.o
$ sed -f q4 rsfit_mc.o > q5 ; mv q5 rsfit_mc.o
$ sed -f q4 rsfit_sc.o > q5 ; mv q5 rsfit_sc.o
$ sed -f q4 pepflip.o > q5 ; mv q5 pepflip.o
$ sed -f q4 rsc.o > q5 ; mv q5 rsc.o
!
print ... datablocks written
!
! list datablock files and remove temporary files
!
$ \ls -al resnam.o restyp.o rsfit_*.o pepflip.o rsc.o
$ /bin/rm q[2-5]
!
! read the datablocks for our real molecule
!
print ... reading datablocks for $mymol
read rsfit_all.o
read rsfit_mc.o
read rsfit_sc.o
read pepflip.o
read rsc.o
!
! delete our temporary molecule JUNKY
!
print ... deleting molecule JUNKY
del_obj junky ;
db_kill junky_*
!
bell
print ...
# Type "save" if you want to save your database now ... #
!
$ echo "... pre_oops.omac stopped at " `date` >> q1
$ cat q1
$ /bin/rm q1
!
bell message Done