• Summary
• A basic script
• Notes on input/output mtz files
• Keywords for resolve

Summary

To run resolve, you need:

• SOLVE and resolve installed on your computer
• the CCP4 suite installed on your computer (or at least the file "symop.lib" somewhere)
• A CCP4 mtz file with at least FP, PHI, FOM for your dataset
• An estimate of the solvent content of your crystal
• To set the CCP4 environmental variables for file control and symmetry (modifying as appropriate for the location of symop.lib on your system):

setenv SYMOP /usr/local/lib/ccp4/symop.lib
setenv CCP4_OPEN UNKNOWN

The most basic resolve script  (see the sample scripts for more cases):
 

#!/bin/csh
#
# Here is a minimal script to run resolve on MAD/MIR/SAD etc data:
#
# 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
hklin solve.mtz
LABIN FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
hklout resolve.mtz
solvent_content 0.4             ! your solvent content goes here.
EOD
#
# Now "resolve.mtz" has the output amplitudes, phases,
# and figure of merit in columns labelled: FP PHIM FOMM.  
#

• Resolve will read from "solve.mtz" and write out new structure factor amplitudes and phases.
• If you have a file "ha.pdb" in your directory, resolve will try to use the PDB coordinates in it to identify and apply NCS.
• Additionally, Hendrickson-Lattman coefficients are written.
• You can use "resolve.mtz" in the same way as you use any mtz file in the CCP4 suite.

Notes on input and output mtz files (see the sample scripts )

• Resolve expects to read data from a CCP4 mtz file
• at least FP, PHI, FOM are needed for MAD/MIR/SAD data
• for prime-and-switch, you need FP FC PHIC FOM, with optional FWT (from sigmaa)
• it works much better for MAD/MIR/SAD data if you also input Hendrickson-Lattman coefficients (HLA HLB HLC HLD)
• you specify the columns with the LABIN keyword as in the CCP4 suite
• (LABIN FP=yourFPcolumn PHIB=yourPHIBestcolumn FOM=yourFOMcolumn HLA=yourHLAcolumn etc)
• If your input file has reflections with non-zero F within your resolution range, it will automatically attempt to phase all of them.
• Resolve will write a CCP4 mtz file
• The output columns of data are H K L  FP PHIM FOMM HLAM HLBM HLCM HLDM
• FP is just what was input
• PHIM is the modified "best" or centroid phase
• FOMM is the figure of merit of PHIM.  Use in a map with F = FP * FOMIM * exp(i PHIM).
• HLAM, HLBM, HLCM, HLDM are Hendrickson-Lattman coefficients for the final phases.

Keywords for resolve

KEYWORD         DEFAULT                 WHAT IT IS

access_file     solve2.access            Name of solve2.access file.  If it is not in the
                                              /usr/local/lib/solve/ directory or in the
                                              current directory or in the directory $SOLVEDIR
                                              then you will want to tell resolve where it is 

hklin           solve.mtz               mtz file with input phases and phase probabilities

hklout          resolve.mtz             mtz file with output phases

LABIN FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
                                        LABIN statement identifying the columns of 
                                        data in the hklin mtz file

LABIN FP=FP FC=FC PHIC=PHIC FOM=WCMB  FWT=FWT    LABIN statement suitable for prime-and-switch. 
                                        FWT is optional; if present initial map calculated with FWT exp(i PHIC).


mask_cycles     5                       Number of cycles in which masks are redone and
                                        images are compared to map

minor_cycles    10                      Number of minor cycles per mask_cycle


prime_and_switch                        Use prime-and-switch phasing. Use input phases only to calculate initial map. 
                                        Input phase probabilities not used at all.

no_erase_protein                        Do not let P(protein) be less than the starting value in prime-and-switch phasing.

solvent_content 0.3                     Fraction of unit cell in solvent region

resolution                              Resolution limits (default=whatever is in input mtz file)

wang_radius                             (default varies with resolution and FOM)
                                        Radius (A) for averaging rms density in Wang method for getting solvent mask

hklstart                                mtz file with a starting set of phases. Resolve will start with
                                        these phases (but use probabilities from hklin).  Useful for
                                        running a few cycles, getting an output resolve_1.mtz, then
                                        continuing on from there.  Goes with labstart. 

labstart  FP=FP PHIB=PHIB FOM=FOM       LABIN statement for hklstart.  only PHIB and FOM used.

cc_ratio      0.1                       Cut off prime-and-switch phasing at resolution where CC 
                                        of FP with FC < cc_ratio

verbose                                 print out a lot of data every cycle, not just at first and last.

nohl                                    don't calculate HL coefficients at end of resolve

rota_matrix                             rotation matrix for NCS symmetry. Three rota_matrix lines define a matrix:
                                        rEnter the identity as first molecule 1.
                                        rota_matrix 1 0 0
                                        rota_matrix 0 1 0
                                        rota_matrix 0 0 1
                                        The rotation matrix applies to orthogonal Angstrom coordinates.
                                        The matrix and translation maps molecule j on to molecule 1.
                                        This is what you get from the ccp4 program lsqkab if molecule 1 is
                                        the reference (xyzin1) and molecule j is the working molecule (xyzin2)

tran_orth                               Translation vector for NCS symmetry element, in orthogonal Angstroms
                                        Enter after rota_matrix

center_orth                             Approximate center of mass of NCS symmetry element, in orthogonal Angstroms
                                        Enter after rota_matrix. Required only for element 1

fraction_ncs  0.15                      fraction of asymmetric unit occupied by 1 molecule (default = fraction protein / N )

invert                                  Invert NCS matrices (they correspond to mapping molecule 1 on to molecule j)

ncs_begin  mask_cycle small_cycle       Begin using NCS on mask cycle mask_cycle, small cycle small_cycle
                                        Resolve works best if the solvent-flattening is mostly done before starting NCS
                                        Default is to start halfway through first mask_cycle if solvent content <50%, halfway
                                          through second mask_cycle if solvent content is 50% or greater.

fix_ncs                                 Do not refine NCS operators

force_ncs                               Use input or heavy-atom-site NCS symmetry even if there is very low correlation

ha_file    ha.pdb                       Use the entries in this file (PDB format) to look for non-crystallographic symmetry

no_find_ncs                             Don't try to find NCS from heavy-atom sites even if the file "ha.pdb" exists