Quick Start

How to use RESOLVE

You can run RESOLVE right after SOLVE (using solve.mtz as input), or you can run it using an mtz-format file written by another program.

Usually if you have MAD/SAD/MIR data, you will want to (1) edit and run one of the standard SOLVE scripts( to solve your structure and calculate an initial map, and (2) edit and  run the RESOLVE_BUILD script to density modify the map and build an atomic model. With fast model-building, the whole process only takes a few hours for a small protein.

If you have an MR model and FOBS data, you will want to run the RESOLVE_BUILD script to remove model bias and build a new atomic model.

If you have non-crystallographic symmetry, you will want to include that in your RESOLVE scripts, either by specifying the NCS matrices (see  Keywords  for resolve) or by specifying the coordinates of some of the atoms in each monomer with a PDB file "ha.pdb" (this can be the heavy-atom file written by SOLVE for MIR/MAD/SAD data, or a file you create from some of the CA atoms in  your starting PDB file for your MR solution).

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/solve/symop.lib

setenv SYMINFO /usr/local/lib/solve/syminfo.lib

setenv CCP4_OPEN UNKNOWN

# Now run RESOLVE:

resolve<<EOD

solvent_content 0.4             ! your solvent content goes here.

!             Next line is protein sequence file

seq_file protein.seq 

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

# Also resolve.pdb contains your model and the heavy-atom sites from SOLVE.

#

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.
• RESOLVE will build a model of your structure into the density after doing statistical density modification.  If you specify seq_file, then it expects a file with the sequence of your protein (1-letter code);  if your protein has more than one unique chain, separate them with a line starting with the characters ">>>".  No need to enter multiple copies of the same chain.
• Resolve will initially use only data in the resolution range where the starting figure-of-merit is significant, then will carry out phase extension.