In this example file, three copies of the molecules have been placed correctly in the unit cell. We are searching for the orientation and position of a fourth molecule. Note that in this case, both the Patterson-correlation TF and the phased TF can be used as the target. The phase information will be based on the molecules that have already been placed in the unit cell.

!
! Input file name: como5.inp
!
title Structure factor calculation for four 3eca monomers
!
print como5.prt
polar xzk
euler zyz
ortho axabz 
!
crystal
   cell   76.700   96.100  111.300  90.00  97.10  90.00 P 21          8  3ECA 310
   fobs 3eca.cal
   format 3i4, f8.2, 8x, f8.2
   frejection 1.0 1.0 0.
   resolution 20 3.5
   symm p21
   end
!
model 
   bover 25                                      ! assign overall B value
   input 3ecam.pdb                               ! read in PDB file
   center                                        ! center model at 0 0 0 
!
   duplicate 1 2                                 ! duplicate molecule
   duplicate 1 3                                 ! duplicate molecule
   duplicate 1 4                                 ! duplicate molecule
!
   rotate 257.750   26.000  264.875 euler        ! rotate molecule
   translate 0.3281    0.0000    0.1146 df       ! translate molecule
   add 1000                                      ! add 1000 to residue number
   flag t                                        ! assign flag, known orientation and position
   swap 1 2                                      ! swap molecule information
!
   rotate 251.812   32.000  259.562 e            ! rotate new molecule
   translate 0.8750    0.5000    0.6198  df      ! translate molecule
   flag t                                        ! assign flag
   chain c                                       ! assign chain name C to this molecule
   swap 1 3                                      ! swap information
!
   rotate 36.250   71.500  320.625 e             ! rotate new molecule
   translate 0.0312    0.7222    0.2656 df       ! translate
   flag t                                        ! assign flag
   add 3000                                      ! add 3000 to residue number
   swap 1 4                                      ! swap
!
   flag u                                        ! assign flag
   end
!
rf
   cutoff 0.25 0.5                              ! large-term cutoff for RF
   fast true                                    ! use the Crowther fast RF
   normalize true 8                             ! normalize the structure factors
   sangle euler                                 ! search in Eulerian angles
   origin true                                  ! remove Patterson map origins
   resolution 10 3.5 ! 10 4.0                   ! resolution range
   radius -1                                    ! radius will be selected by program
   save 10                                      ! identify the top 10 peaks in RF
   end
!
tf
   cutof 2 0.5                                  ! large-term cutoff for TF
   dcutoff 3                                    ! distance cutoff for packing check
   resolution 10 3.5
   save 20 true                                 ! identify top 20 peaks in each TF
   solution 1                                   ! save top peak as MR solution
   flag a                                       ! search for all molecules
   rigid true                                   ! do a rigid-body optimization
!  target ecec                                  ! Phased translation function
   select 0.8 1 0                               ! RF selection for search of 4th copy
   end
!
solution
  file como5.pdb                                ! write MR solution to this file
  dcut 3
  end
!
stop

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