#  command file to solve a 2-deriv MIR dataset + anom diffs in native


# CCP4_OPEN environmental variable set to UNKNOWN so file overwriting will work
setenv CCP4_OPEN UNKNOWN

solve <<***
!   solve a 2-deriv MIR dataset + anom diffs in native
@solve.setup                   ! get our standard information read in
logfile mir.logfile            ! write out most information to this file.
                               ! summary info will be written to solve.prt

readformatted                  ! alternatives are readdenzo, readtrek
premerged                      ! alternative is unmerged
read_intensities               ! alternative is read_amplitudes

rawnativefile lam1.intensities ! native data

! now read in native data again as a pseudo-deriv 1:
! put in scattering factors for pseudo-atom fel1 with only ano
! scattering

newatomtype FEL1
aval 0 0 0 0
bval 0 0 0 0
cval 0.001
fprimv 0 
fprprv 3

derivative 1
label native data with ano diffs, treated as deriv 1
nsolsite_deriv 1               ! just 1 site
rawderivfile lam1.intensities
inano
anoonly                        ! no isomorphous diffs, just ano
atomname fel1                  ! use our pseudo-atom with no iso scattering

! now read in the regular 2 derivs:
derivative 2                   ! about to enter information on derivative #1
label deriv 1 HG               ! a label for this deriv
nsolsite_deriv 1               ! one site in this deriv
rawderivfile der1.intensities  ! data from generate.com
inano                          ! You need to tell it if anomalous diffs are
                               ! to be used
noanorefine                     ! do not use ano diffs for refinement 
atomname Hg                   ! tell SOLVE what the heavy atom is

derivative 3
label deriv 2 also hg
rawderivfile der2.intensities        ! the derivative data is in this file
nsolsite_deriv 2
inano
noanorefine                     ! do not use ano diffs for refinement 
atomname hg
acceptance 0.35                 ! accept a new site if it has a
                                ! peak height about 1/3 of avg or more
SCALE_NATIVE                    ! scale the native dataset
SCALE_MIR                       ! scale the derivs to the native
ANALYZE_MIR                     ! analyze this mir data and set up for SOLVE
SOLVE
***