What can I do with results from SHARP?

Contents

• resid.mtz
• eden.mtz
• eden-unique.mtz
• eden_flat_<solvent fraction>pc.mtz
• wARP_<solvent fraction>pc.mtz
• model_<project>.<id>_wARP_<solvent content>pc.pdb

resid.mtz

	CC :	compound number
	XX :	crystal number
	WW :	wavelength number
	BB :	batch number
	SRC :	source of gradient or model information
		ISO :  isomorphous/dispersive differences between this dataset and the reference dataset ANO :  anomalous differences within this dataset
	TYP :	type of map
		HAT :  heavy atom model map for this dataset RES :  log-likelihood gradient residual map
	RI :	real or imaginary part
		RL :  real part IM :  imaginary part

Column	Type	Description
H, K, L	Miller indices
CC_XX_WW_BB_ISO_HAT__F	real	amplitude of calculated heavy atom density for isomorphous/dispersive difference
CC_XX_WW_BB_ISO_HAT__P	real	phase of calculated heavy atom density for isomorphous/dispersive difference
CC_XX_WW_BB_ISO_RES__F	real	amplitude of residual map for isomorphous/dispersive difference
CC_XX_WW_BB_ISO_RES__P	real	phase of residual map for isomorphous/dispersive difference
CC_XX_WW_BB_ANO_HAT__F	real	amplitude of calculated heavy atom density for anomalous difference
CC_XX_WW_BB_ANO_HAT__P	real	phase of calculated heavy atom density for anomalous difference
CC_XX_WW_BB_ANO_RES__F	real	amplitude of residual map for anomalous difference
CC_XX_WW_BB_ANO_RES__P	real	phase of residual map for anomalous difference

These columns can be used in a variety of ways:

1. calculation of heavy atom maps: this is done with columns CC_XX_WW_BB_ISO_HAT__F/CC_XX_WW_BB_ISO_HAT__P or CC_XX_WW_BB_ANO_HAT__F/CC_XX_WW_BB_ANO_HAT__P. To do this in the CCP4 program FFT:

         fft hklin resid.mtz mapout 01_01_02_01_ISO_HAT.map <<end_ip
         LABI F1=01_01_02_01_ISO_HAT__F PHI=01_01_02_01_ISO_HAT__P
         end_ip
         

   This would calculate a heavy atom model map for wavelength 2 in the first crystal of the first compound (e.g. the second wavelength in a MAD experiment), based on dispersive differences.

2. calculation of residual maps: this is done with columns CC_XX_WW_BB_ISO_RES__F/CC_XX_WW_BB_ISO_RES__P or CC_XX_WW_BB_ANO_RES__F/CC_XX_WW_BB_ANO_RES__P. To do this in the CCP4 program FFT:

         fft hklin resid.mtz mapout 01_01_01_01_ANO_RES.map <<end_ip
         LABI F1=01_01_01_01_ANO_RES__F PHI=01_01_01_01_ANO_RES__P
         end_ip
         

   This would calculate an anomalous log-likelihood gradient residual map for the first dataset/batch in the first crystal of the first compound (e.g. the anomalous data in a SAD experiment).

eden.mtz

Column	Type	Description
H, K, L	Miller indices
FP	amplitude	"native", unperturbed structure factor amplitude
SIGFP	standard deviation	standard deviation of FP
HLA, HLB, HLC, HLD	Hendrickson-Lattman coefficients	description of phase probability
FB	amplitude	centroid electron density structure factor amplitude
PHIB	phase	centroid electron density structure factor phase
FOM	figure-of-merit
NUMORB		multiplicity description

These columns can be used in a variety of ways:

1. calculation of electron density maps: this is done with amplitude FB and phase PHIB (no need to include a weight like FOM). To do this in the CCP4 program FFT:

         fft hklin eden.mtz mapout eden.map <<end_ip
         LABI F1=FB PHI=PHIB
         end_ip
         

2. density modification: the starting map should always be calculated using FB/PHIB. The native structure factor amplitudes (and its standard deviation) are FP/SIGFP. For phase combination, the Hendrickson-Lattman coefficients HLA, HLB, HLC and HLD are used. A (typical) DM run could look like this:

         dm hklin eden.mtz hklout dm.mtz <<end_ip
         SOLC 0.50
         LABI FP=FP SIGFP=SIGFP PHIO=PHIB FOMO=FOM -
              HLA=HLA HLB=HLB HLC=HLC HLD=HLD -
              FDM=FB PHIDM=PHIB
         LABO FDM=FDM PHIDM=PHIDM
         end_ip
         

   (please check your documentation for complete syntax)

   Note : the phase improvement and interpretation tools provided through the interface (e.g. using SOLOMON for solvent flattening) are highly optimised for use with SHARP. We strongly recommend the use of these for phase improvement after phasing with SHARP. However, if you find a program/strategy that performs better in your particular case, we would be glad to hear about it.

eden-unique.mtz

eden_flat_<solvent fraction>pc.mtz

Column	Type	Description
H, K, L	Miller indices
FPsha	amplitude	"native", same as FP in eden.mtz
SIGFPsha	standard deviation	standard deviation of FPsha (same as SIGFP in eden.mtz)
HLA, HLB, HLC, HLD	Hendrickson-Lattman coefficients	description of phase probability (same as in eden.mtz)
FBsha	amplitude	centroid electron density structure factor (including average heavy atom contribution) amplitude (same as FB in eden.mtz)
PHIBsha	phase	centroid electron density structure factor (including average heavy atom contribution) phase (same as PHIB in eden.mtz)
FOMsha	figure-of-merit	(same as FOM in eden.mtz)
FreeR_flag	test flag
FBshasol	amplitude	solvent flattened structure factor (including average heavy atom contribution) amplitude
PHIBshasol	phase	solvent flattened structure factor (including average heavy atom contribution) phase
Fcentshasol	amplitude	solvent flattened structure factor (light atoms only) amplitude
PHIcentshasol	phase	solvent flattened structure factor (light atoms only) phase
PHIshasol	phase	combined phase
FOMshasol	weight	combined figure-of-merit
HLAshasol, HLBshasol, HLCshasol, HLDshasol	Hendrickson-Lattman coefficients	description of phase probability (after density modification with SOLOMON)

These columns can be used to calculate solvent flattened electron density maps, e.g. with the CCP4 program FFT:

fft hklin eden_flat_50.0pc.mtz mapout eden_flat_50.0pc.map <<end_ip
LABI F1=FBshasol PHI=PHIBshasol
end_ip

wARP_<solvent fraction>pc.mtz

Column	Type	Description
H, K, L	Miller indices
FPsha	amplitude	"native", unperturbed structure factor amplitude (same as FP in eden.mtz)
SIGFPsha	standard deviation	standard deviation of FPsha (same as SIGFP in eden.mtz)
FreeR_flag	test flag
FC	amplitude	calculated structure factor amplitude of (auto-built) model
PHIC	phase	calculated structure factor phase of (auto-built) model
2FOFCWT	amplitude	Fourier amplitude for (2mFo-DFCalc) map
PH2FOFCWT	phase	Fourier phase for (2mFo-DFCalc) map
FOFCWT	amplitude	Fourier amplitude for (mFo-DFCalc) map
PHFOFCWT	phase	Fourier phase for (mFo-DFCalc) map
FOM	figure-of-merit
PHCOMB	phase	combined (with experimental phases from SHARP) phase

(see also your local documentation for REFMAC)

The best electron density map can be calculated with FFT:

fft hklin wARP_50.0pc.mtz mapout wARP_50.0pc.map <<end_ip
LABI F1=2FOFCWT PHI=PH2FOFCWT
end_ip

model_<project>.<id>_wARP_<solvent content>pc.pdb

• <project>.<id> is the project and run identifier that point to the sharpfiles/logfiles/<project>.<id> directory
• <solvent content> has the same meaning as in the corresponding MTZ file (wARP_<solvent fraction>pc.mtz)