Crystallography‎ > ‎Phasing‎ > ‎

SOLVE/RESOLVE


Run solve/resolve through phenix (http://www.phenix-online.org/documentation/running-solve-resolve.htm)


Type: 

phenix.solve < phenix.eff

Where phenix.eff is something like this (SAD example):

@solve.setup
logfile solve.logfile
readdenzo
premerged
read_intensities
fixscattfactors
RES_PHASE 3.0
resolution 100.0 2.3
mad_atom Se
lambda 1
wavelength  0.97650
fprimv_mad   -8.0
fprprv_mad    4.0
rawmadfile output.sca
ATOMNAME Se
anoonly
nres 500
nanomalous 5
SAD
solve

The @solve.setup will be a file (called solve.setup) that looks like this:

!------------------ solve.setup: standard setup for a dataset --------------
SYMFILE ./p43.sym
CELL 58.280    58.280   129.906    90.000    90.000    90.000 p4
RESOLUTION 2.3 50.00
FFTGRID  0 0 0 0 0 0 0 0 0
PATTGRID 0 0 0 0 0 0 0 0 0
EZGRID 0 0 0 0 0 0 0 0 0

The .sym file needed for the first row (SYMFILE) can be found in the phenix folders (ie /usr/local/phenix-1.6.1-357/solve_resolve/ext_ref_files).

Once solve is finished, it is possible to run resolve as:

phenix.resolve << EOD

Then copy and paste the following after the ">":

hklin solve.mtz labin FP=FP SIGFP=SIGFP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD 
solvent_content 0.43 
database 5 
seq_file protein.seq ! See below how the seq file should me formatted
EOD


SOLVE output


Monitor output of solve:

tail -30f solve.status

correct solutions will have:

peaks heights for all HAs more than 5 or 10 sigma
high Z-score (>20)
figure of merit (m) around 0.6 to 0.7

From the manual:

The solve.status file can give you a pretty good indication of whether SOLVE has found a good solution. A correct solution will have high values of peak heights for all the heavy atom sites in the cross-validation difference Fouriers (for most good solutions these peak heights will all be more than 5 or 10 sigma). A good solution will have a high Z-score (typically above 20; this score is higher for structures with more heavy atoms). A good solution will have a figure of merit around 0.6 to 0.7 as well.

Examples from successful runs:

- Mine:

***************************************************************************
SOLVE STATUS 23-feb-11 17:22:27

DATASET TITLE: SOLVE 23-Feb-11
TIME ELAPSED: 2 MIN

---------------------------------------------------------------------------
CURRENT STEP:SOLVE MAIN PROGRAM
STATUS: DONE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
---TOP SOLUTION FOUND BY SOLVE (<m> = 0.34; score = 20.18) ---

  X     Y     Z     OCCUP B    HEIGHT/SIGMA

1 0.622 0.809 0.249 0.531 56.5 16.4
1 0.232 0.684 0.007 0.498 37.5 18.4
1 0.947 0.740 0.008 0.365 46.9 14.9
1 0.689 0.831 0.229 0.323 52.0 12.3
1 0.973 0.728 0.047 0.451 60.0 11.4
1 0.950 0.650 0.032 0.225 53.3 7.1
1 0.223 0.259 0.037 0.115 29.4 5.1

TIME REQUIRED TO OBTAIN THIS SOLUTION: 2 MIN
---------------------------------------------------------------------------

- ?:

*******************************************************
SOLVE STATUS 06-aug-09 11:36:56 

DATASET TITLE: SOLVE 06-Aug-09 
TIME ELAPSED: 11 MIN

---------------------------------------------------------------------------
CURRENT STEP:SOLVE STEP TIME: 11 MIN
STATUS: Evaluated soln 9 for seed 4 in SOLVE. Score: 11.69 
---------------------------------------------------------------------------
---------------------------------------------------------------------------
---TOP SOLUTION FOUND BY SOLVE (<m> = 0.19; score = 17.11) 

  X     Y     Z     OCCUP B   HEIGHT/SIGMA

1 0.994 0.106 0.031 0.423 1.0  7.7
1 0.042 0.576 0.010 0.354 1.0  6.3
1 0.014 0.073 0.032 0.443 3.5  7.6
1 0.920 0.454 0.010 0.372 37.8 4.1
1 0.420 0.406 0.023 0.040 1.0  4.2
1 0.064 0.115 0.041 0.257 1.0  3.1
1 0.646 0.893 0.056 0.190 1.0  5.6
1 0.414 0.933 0.047 0.230 1.0  5.7
1 0.721 0.551 0.023 0.646 50.3 6.8
1 0.202 0.412 0.248 0.065 1.0  4.2
1 0.500 0.990 0.104 0.390 60.0 4.7
1 0.030 0.931 0.093 0.014 1.0  5.9
1 0.551 0.435 0.116 0.193 31.1 3.9

TIME REQUIRED TO OBTAIN THIS SOLUTION: 8 MIN


RESOLVE after SOLVE


Minimal script for running resolve:

#!/bin/csh
# Here is a 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 ! Solvent content goes here
seq_file protein.seq ! See below how the seq file should me formatted
EOD

RESOLVE assumes "solve.mtz" as input with FP PHIB FOM HLA HLB HLC HLD.
Output is "resolve.mtz" with FP PHIM FOMM HLAM HLBM HLCM HLDM (M is for modified).
You need to tell RESOLVE the solvent content (approximately).
If you want to save time and do not want a model, specify the keyword: no_build

The sequence file for your protein should look like:

MIVLTVHYSSEGILV [put the sequence of chain type 1 here, up to 80 characters per line]
>>> [this defines the end of chain 1]
MKLVERWISSTV [put the sequence of chain type 2 here, up to 80 characters per line]

LINKS


Solve manual: 

Resolve manual: