• How to run resolve right after SOLVE
• How to use prime-and-switch phasing to remove model bias from a map

Running resolve right after SOLVE

It is really easy to run resolve right after SOLVE. Just go to the directory where you ran SOLVE and type (or put in a command file):

#!/bin/csh
# Here is a very 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.
EOD
# Now "resolve.mtz" has the output amplitudes, weighted F, phases,
# figure of merit and HL-coeffs in columns labelled: FP PHIM FOMM HLAM HLBM HLCM HLDM
#

That's it! (Sure, there are a few other keywords, but usually you don't need them.) (More sample scripts are available too.)

• 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.
• The new phases are called PHIM and the figure of merit is FOMM (M is for modified).
• If there is a file called "ha.pdb" in your working directory, resolve will assume it contains heavy-atom sites in PDB format and will try to find NCS in them and to apply it if it exists.  It will ignore the NCS if the correlation is very low.

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Removing model bias with prime-and-switch phasing

Prime-and-switch phasing starts with the best phase set you have (usually sigma-A phasing based on your model). A map is calculated, and the probability that each point in the map is in solvent/macromolecule regions are identified.  Then the phases are adjusted to improve the agreement of the electron density in the map with expected electron density distributions, without using the input phase probability distributions any more.

To carry out prime-and-switch phasing:

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 resolve.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
#

That's it! (More sample scripts are available too.)

• Resolve will read from "sigmaa.mtz" and write out new structure factor amplitudes and phases to "ps.mtz."
• You can use "resolve.mtz"  in the same way as you use any mtz file in the CCP4 suite.
• The new phases are called PHIM and the figure of merit is FOMM (M is for modified).