The minimal script for running resolve (on experimental data)
Keywords for running resolve with a different input file
Running resolve with different numbers of cycles or resolution
Running resolve with NCS
Prime-and-switch phasing starting from a SIGMAA-weighted map
 
 

The minimal script for running resolve: (Some sample data and input files are located the library directory where SOLVE and resolve are installed, usually located at /usr/local/lib/solve/solve-2.00/lib/examples_resolve/ )
 
 

#!/bin/csh
#
# Here is a minimal script to run resolve:
#
# Set CCP4 variables for symmetry information and
# for file handling:
#
setenv SYMOP /usr/local/lib/ccp4/symop.lib
setenv CCP4_OPEN UNKNOWN
#
# Now run resolve:
#
resolve<<EOD
solvent_content 0.4             ! your solvent content goes here. That's all you need.
EOD

• Resolve assumes "solve.mtz" as input with FP PHIB FOM HLA HLB HLC HLD
• Output is "resolve.mtz" with FP PHIM FOMM HLAM HLBM HLCM HLDM  (M is for modified)
• You need to tell resolve the solvent content (approximately)

Keywords for running resolve with a different input file:
 
 

hklin other.mtz
LABIN FP=F PHIB=PHI FOM=W HLA=HLA HLB=HLB HLC=HLC HLD=HLD
hklout resolve.mtz
solvent_content 0.4             ! your solvent content goes here.

• The input file is named with HKLIN
• The column names can be specified with the LABIN keyword
• The output file can be specified with the HKLOUT keyword.

Running resolve with a different number of cycles or changing resolution:
 
 

mask_cycles 4                   ! number of cycles of solvent mask generation (default = 5)
minor_cycles 3                  ! cycles of iteration for each mask cycle (default = 10)
solvent_content 0.4             ! your solvent content goes here.mask_cycles 4                   ! number of cycles of solvent mask generation
resolution 20 3.5               ! You can limit the resolution if you want

• You might want fewer mask cycles to save time if the phase change in the last cycles is very small.
• Alternatively you might want more minor cycles for each mask cycle if the phase change in the last minor cycles of each mask cycle is not very small.
• You can limit the resolution if you want. Currently, resolve does not fill in reflections that are not in the input file.  Resolve will fill in phase information  for any reflections that it reads in that have a non-zero structure factor amplitude

 

 
 

Running resolve with NCS

Alternatively, you can enter NCS operators directly to resolve.  In this case you also need to enter  an estimate of the center-of-mass of molecule 1.

You need to input N sets of rotation matrices/translations/centers-of-mass, 1 for each copy in the asymmetric unit. Start with the identity for molecule 1.  You can conveniently get all the numbers you need from the CCP4 program lsqkab if you have a model that you are starting with. The rotation/translation matrices and the center-of-mass are all input in a form appropriate for operating on orthogonal Angstrom coordinates (not fractional coordinates).

        rota_matrix  .92  .01  .33         !rotation matrix for molecule j ->molecule 1
        rota_matrix -.01 -.99  .03
        rota_matrix  .05  .10 -.95
        tran_orth    .50  .00 .00          ! translation for molecule j -> molecule 1
        center_orth   25.  39. 44.         !  center of mass, molecule j

        fraction_ncs 0.15                  ! fraction of the asymmetric unit in 1 copy of NCS
                        ! (only needed if it is not equal to (fraction protein)/(number of NCS copies)

 
•  Resolve automatically identifies a mask for NCS, but requires an estimate of the center of molecule 1, in orthogonal A units ("center_orth")
•  Resolve expects rotation matrices ("rota_matrix") and translation vectors ("trans_orth")  in orthogonal Angstrom units that map each of the N molecules onto molecule 1 in the asymmetric unit.  This is the form produced by the CCP4  program lsqkab with xyzin1 (reference)= molecule 1 and xyzin2 (working)= molecule j. If you have transformations that go from molecule 1 to molecule  N, you can specify "invert" to invert the transformations.
• Input the matrices first (three lines of "rota_matrix" for each matrix); then the translation vector
• Input the identity as the first rotation matrix, with a zero translation vector
• For at least the first molecule, you need to enter an estimate of the center of the molecule ("center_orth"). If you enter centers for others, resolve will verify that the centers match the positions expected from the symmetry you input

Prime-and-switch phasing starting from a SIGMAA-weighted map

To carry out prime-and-switch phasing starting with phases calculated from a model:  (Sample data and input files are located the library directory where SOLVE and resolve are installed, usually located at /usr/local/lib/solve/solve-2.00/lib/examples_resolve/ )

1. Run Randy Read's SIGMAA program to get as unbiased a starting map as possible into "sigmaa.mtz"
2. Go to the directory where you ran sigmaa and type (or put in a command file):
 

#!/bin/csh
# Here is a very minimal script to run prime-and-switch phasing
#
# Set CCP4 variables for symmetry information and
# for file handling:
#
setenv SYMOP /usr/local/lib/ccp4/symop.lib
setenv CCP4_OPEN UNKNOWN
#
# Now run prime-and-switch phasing:
#
resolve<<EOD
hklin sigmaa.mtz
labin FP=FP FC=FC PHIC=PHIC FOM=WCMB FWT=FWT
hklout ps.mtz
solvent_content 0.4 ! your solvent content goes here.
prime_and_switch
EOD
#
# Now "ps.mtz" has the output amplitudes, phases,
# figure of merit and HL-coeffs in columns labelled: FP PHIM FOMM HLAM HLBM HLCM HLDM
#

Note:  The least biased map from SIGMAA is FWT exp(i PHIC), so resolve works best starting with FWT from SIGMAA.  However, you can leave out FWT if you wish. You need FP FC PHIC at a minimum.