Summary

To run resolve, you need:

• Resolve installed on your computer
• SOLVE 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/ccp4/lib/data/symop.lib
setenv CCP4_OPEN UNKNOWN

You can run resolve with a command file that looks like this (more sample scripts are also available)
 
 

#!/bin/csh
#
# Here is a minimal script to run resolve:
#
# Set CCP4 variables for symmetry information and
# for file handling:
#
setenv SYMOP /usr/local/ccp4/lib/data/symop.lib
setenv CCP4_OPEN UNKNOWN
#
# Now run resolve:
#
resolve<<EOD
hklin solve.mtz
labin   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 to "resolve.mtz."
• You can use "resolve.mtz" in the same way as you use any mtz file in the CCP4 suite.

Input and output mtz files

• Resolve expects to read data from a CCP4 mtz file
• at least FP, PHI, FOM are needed
• it works much better 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)
• Resolve will write a CCP4 mtz file
• The output columns of data are H K L FP PHIM FOMM
• FP is just what was input
• PHIM is the modified "best" or centroid phase
• FOMM is the figure of merit of PHIM
• To use this to calculate a map, use FOMM as the weight.

Keywords for resolve

KEYWORD         DEFAULT                 WHAT IT IS

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


hklin           solve.mtz               mtz file with input phases

hklout          resolve.mtz             mtz file with output phases


labin   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

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


model  model.pdb5      PDB file used to calculate model density for
 region containing macromolecule. Phases are adjusted to match this
 density as closely as possible.  Use with "noprior"


noprior                               Do not use input phases and weights for anything; 

noprotein                               Do not use histograms of protein region 


noscale                                 Do not scale the data

nosharpen       (default)               Do not sharpen the data

nosolvent                               Do not use solvent flattening


prot_scatt      0.43                    Mean electron density in protein

protein         (default)               Use histograms of protein region

scale           (default)               Scale the data

sharpen                                 Sharpen the data

solv_scatt      0.32                    Mean electron density in solvent

solvent         (default)               Use solvent flattening

solvent_content 0.3                     Fraction of unit cell in solvent region

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