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Sample scripts for resolve

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
Iterative model-building and refinement with RESOLVE and refmac5
 
 

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-2.03/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. Next line is your sequence file
seq_file protein.seq
EOD
  • If you want to save time and do not want a model, specify the keyword: no_build
  • The sequence file for your protein should look like:
  • MIVLTVHYSSEGILV   [put the sequence of chain type 1 here]
    >>>      [this defines the end of chain 1]
    MKLVERWISSTV      [put the sequence of chain type 2 here]
    NOTE: just input 1 copy of each unique chain
     
     

    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. Next line is your sequence file
    seq_file protein.seq


    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. Next line is your sequence file
    seq_file protein.seq
    mask_cycles 4                   ! number of cycles of solvent mask generation
    resolution 20 3.5               ! You can limit the resolution if you want
    Running RESOLVE with NCS
    You can have RESOLVE identify NCS from atoms in a PDB file (default file is the "ha.pdb" file output by SOLVE). You can also generate an appropriate file for molecular replacement cases by selecting 3 equivalent atoms in each molecule and creating a PDB file with just these 3*N atoms.

    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)

     

    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-2.03/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. Next line is your sequence file
    seq_file protein.seq
    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.
     

  • Output is "resolve.mtz" with FP PHIM FOMM HLAM HLBM HLCM HLDM  (M is for modified)

  • Iterative model-building with RESOLVE and refmac5

    You can carry out model-building and refinement iteratively with RESOLVE and refmac5 .  A script that will do it for you is resolve_autobuild.csh.