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Running RESOLVE


Summary

To run RESOLVE, you need:

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.
             ! Next line is the file with your protein sequence
seq_file protein.seq 
EOD
#
# Now "resolve.mtz" has the output amplitudes, phases,
# and figure of merit in columns labelled: FP PHIM FOMM.  
# A model of your structure is in resolve.pdb.  
#

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

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
no_build                                Don't build a model (you might say this to save time)
seq_file protein.seq                    File containing protein sequence
                                        Format: 1-letter code sequence of each chain, separated 
                                        by lines starting with >>> .  No need to put in duplicate chains.
no_expand_ncs                           Don't expand number of copies of each chain beyond what was found with ha sites
seq_prob_min 0.95                       Minimum confidence of sequence match to place side chains on a fragment
noget_peaks                             Skip searching for helices/strands and use data from peak_file
noget_fragments                         Skip searching for fragments and use data from fragment_file
peak_file      resolve_peaks.dat        Intermediate file with locations of all helices/strands considered
fragment_file  fragments.dat            Intermediate file with coordinates of all fragments considered in model-building
assemble_only                           Just assemble the model and write it out (using info in peak_file and fragment_file)
fom_cut  0.15                           Set initial resolution for density modification to be where the FOM is about .15
s_step   0.02                           Steps in s=1/d to take during phase extension


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)
res_start   2.5                         Start out density modification at this resolution, then extend to maximum

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 (saves time)
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)
fix_ncs                                 Do not refine NCS operators
force_ncs                               Use input or heavy-atom-site NCS symmetry even if there is very low correlation
rad_ncs_mask_max  rad          ha.pdb                 Do not allow NCS mask to have radius greater than rad
ha_file          ha.pdb                 Use the entries in this file (PDB format) to look for non-crystallographic symmetry
compare_file    xxx.pdb                 Use coords in this file to define asymmetric unit for output resolve_compare.pdb
                                        NOTE: has no effect on contents of resolve.pdb
no_find_ncs                             Don't try to find NCS from heavy-atom sites even if the file "ha.pdb" exists
do_all_cycles                           Do all the assigned cycles, even if nothing is happening
no_fill                                 Don't fill in missing reflections (default) (best usually)
fill                                    Fill in missing reflections (risky)