[sharp-discuss] residual map

[Clemens Vonrhein]

Hi,

I attach a README file about the resid.mtz file (this information will
be in the manual for the next Sushi release). Let me know if you need
more information ...

Cheers

Clemens

On Mon, Mar 24, 2003 at 03:30:45PM +0800, chernhoe wrote:
> I would like to know how SHARP calculates residual maps from eg. SAD
> datasets. Specifically, I want to know which column labels from the
> sharp output mtz files to use in FFT (CCP4) to manually calculate an
> anomalous residual map.
> 
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss


resid.mtz

This output file from SHARP contains the columns to calculate
log-likelihood gradient residual maps. The coefficients are stored as
pairs of real/imaginary part of a "structure factor". They follow the
same hierarchical syntax as the Sharp INput file:
CC_XX_WW_BB_SRC_TYP_RI, where

    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_RL	real		real part of calculated heavy
                                        atom density for
					isomorphous/dispersive
					difference 
CC_XX_WW_BB_ISO_HAT_IM	real		imaginary part of calculated
                                        heavy atom density for
					isomorphous/dispersive
					difference 
CC_XX_WW_BB_ISO_RES_RL	real		real part of residual map for
                                        isomorphous/dispersive difference
CC_XX_WW_BB_ISO_RES_IM	real		imaginary part of residual map
                                        for isomorphous/dispersive
                                        difference 
CC_XX_WW_BB_ANO_HAT_RL	real		real part of calculated heavy
                                        atom density for anomalous
                                        difference 
CC_XX_WW_BB_ANO_HAT_IM	real		imaginary part of calculated
                                        heavy atom density for
                                        anomalous difference 
CC_XX_WW_BB_ANO_RES_RL	real		real part of residual map for
                                        anomalous difference
CC_XX_WW_BB_ANO_RES_IM	real		imaginary part 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_RL/CC_XX_WW_BB_ISO_HAT_IM or
      CC_XX_WW_BB_ANO_HAT_RL/CC_XX_WW_BB_ANO_HAT_IM. To do this in the
      CCP4 program FFT:

      fft hklin resid.mtz mapout 01_01_02_01_ISO_HAT.map <<end_ip
      LABI A=01_01_02_01_ISO_HAT_RL B=01_01_02_01_ISO_HAT_IM
      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_RL/CC_XX_WW_BB_ISO_RES_IM or
      CC_XX_WW_BB_ANO_RES_RL/CC_XX_WW_BB_ANO_RES_IM. To do this in the
      CCP4 program FFT: 

      fft hklin resid.mtz mapout 01_01_01_01_ANO_RES.map <<end_ip
      LABI A=01_01_01_01_ANO_RES_RL B=01_01_01_01_ANO_RES_IM
      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).


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