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Re: [ccp4bb]: averaging



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Dear Bernard and Gokulan,


Have you tried using DM or RESOLVE to improve your phases?  Both can start
from a simple model (with DM use lsqkab to get  NCS operators) and perform
iterative rounds of NCS averaging and solvent flattening, which helps if you
have a poor starting model.  I have started to do this for regular model
building, after CNS refinement.  I take a Fo.Fc.phs file from cns and convert
it into an ascii file with

Fo Fc sFc and PhiC
which I then convert into an MTZ file for resolve.  Resolve also needs a few
atoms per monomer to be able to calculate the NCS operators.  Resolve will the
automatically generate a mask based on your ED (not as optimal as a manually
built mask).

  Here is an example script for running RESOLVE:

#!/bin/sh
# Here is a very minimal script to run prime-and-switch phasing
#
# Set CCP4 variables for symmetry information and
# for file handling:
#
#ccp4_setup
#setenv SYMOP /usr/local/lib/solve/symop.lib
#setenv CCP4_OPEN UNKNOWN
##############################################################################

# Use the phase file from CNS  (Fo sFo Fc PhiC)
##############################################################################

.../pmb_cns2phs.pl fo.sfo.fc.fob

##############################################################################

# Convert PHSS file to MTZ
##############################################################################

f2mtz HKLIN new_s.phs HKLOUT new_s.mtz << f2mtz_eof |tee f2mtz.html
TITLE   MTZ from PHSS  Dps T2b3 From FoFc_calc.inp -> pmb_cns2phs.pl
PNAME   D175D3_50
DNAME   D175D3_50
CELL     80.109   80.109   132.296 90 90 120
LABOUT   H  K  L  FO    SIGFO    FC     PHIC
CTYPout  H  H  H  F     Q        F      P
FORMAT '(3F5.0,4F11.3)'
SYMM 154
f2mtz_eof

##############################################################################

# Use SIGMAA to determine phase probabilities
##############################################################################

sigmaa HKLIN new_s.mtz HKLOUT new_sa.mtz << simaa_eof |tee sigmaa_log.html
TITLE   SIGMAA m*Fo-Fc map
###RESOLUTION 500.0 1.9 ! Resolution limits in Angstroms
RANGES   20 5000     ! Number of bins for analysis v. resolution
####                  ! Monitor every 5000th reflection
PARTIAL              ! Option for difference map coefficients
ERROR                ! Use sigmaA v resolution for coordinate error
LABIN   FP=FO  SIGFP=SIGFO  FC=FC  PHIC=PHIC
END
simaa_eof
#
# create the HA.pdb file for NCS
#
grep " CA  ARG [A-C]  28 " minimize.pdb > ha.pdb
grep " CA  ALA [A-C] 138 " minimize.pdb >> ha.pdb
grep " SD  MET [A-C] 185 " minimize.pdb >> ha.pdb
#
##############################################################################

# Now run prime-and-switch phasing:
##############################################################################

resolve <<EOD |tee  resolve_map.log
hklin new_sa.mtz
labin FP=FO  FC=FC PHIC=PHIC FOM=WCMB FWT=FWT
hklout resolve.mtz
solvent_content 0.47           ! your solvent content goes here (lower by 5%
to avoid trimming ED).
prime_and_switch
EOD
# Now "resolve.mtz" has the output amplitudes, phases,
# figure of merit and HL-coeffs in columns labelled: FP PHIM FOMM HLAM HLBM
HLCM HLDM
#
mtz2various HKLIN resolve.mtz HKLOUT resolve_map.phs << mtz2_eof
LABIN FP=FP FOM=FOMM PHIC=PHIM  HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM
OUTPUT USER '(3I5,3F10.3, 4F8.3)'
mtz2_eof
#
echo "Run xfft to create an FSFOUR map file from resolve_map.phs"
#
# Make a fin file from the model phas file to be phased by the resolve map in
xmergephs
#
awk '{printf"%5d%5d%5d%10.3f %8.3f%10.3f %8.3f \n",$1,$2,$3,$4,9.0,$5,9.0}'
083017_.06.pmb_lscale.phs > 083017_.06.pmb_lscale.fin
#





Bernhard Rupp wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Dear All:
>
> Gokulan and I are stuck with what ought to be a simple procedure (harhar)
> Given: a h k l fo, fom, phwt file, warped from a trimer w/o using NCS
> Wanted: a 3-fold averaged map with NCS, in hope to improve weak density.
> Succeeded:
> make a ccp4 map (awk, fft)
> make a cell map (mapmask)
> make a xtalview map (map2fs, thanks Frank!)
> rtftm maprot (t for thin)
> used NCS ops from CNS (probably questionable as the rmsd is 4.5A)
> nevertheless, script made and resulting map has no overlap according
> to log.
> Inspection of input maps satisfactory.
> Transposition of matrix gives same nonsense. Maps look unchanged from input
> map.
>
> I guess the result is Bad news:
>
> Mapping density from cell using operator   1
> Mapping density from cell using operator   2
> Mapping density from cell using operator   3
> Mapping density to cell using operator   1
>    Density correlation:  0.00000  over      0:  0     0:  0     0:  0
> Mapping density to cell using operator   2
>    Density correlation:  0.00000  over    245:245  -113:***   113:113
> Mapping density to cell using operator   3
>    Density correlation:  0.00000  over    -68:-68  -181:***   175:175
>
> Obviously, we are doing something wrong.
> Secondly, is there a better way to get consistent NCS matrices from direct
> manipulation
> of the maps?
> and third, Should a mask be made instead of just copying the CNS ncs
> matrices?
>
> thx, Gokulan and br
>
> INPUT
>
>  Data line--- CELL 83.123 104.872 105.196 90.000 90.000 90.000
>  Data line--- GRID 240 240 240
>  Data line--- MODE BOTH
>  Data line--- SCALE 0.33333
>  Data line--- AVER
>  Data line--- ROTA POLAR  0.0  0.0  0.0
>  Data line--- TRANS  0.0  0.0  0.0
>  Data line--- AVER
>  Data line--- ROTA MATRIX  -0.44014  0.63215 -0.63770 -0.62202  0.29754
> 0.72426 0.64759  0.71544  0.26225
>  Data line--- TRANS  84.76557  -49.18177   49.70381
>  Data line--- AVER
>  Data line--- ROTA MATRIX  -0.51502 -0.63090  0.58027 0.58774  0.23286
> 0.77482 -0.62395  0.74009  0.25088
>  Data line--- TRANS -23.52714  -79.15917   76.67988
>
> is assembled from CNS NCS ops (get_ncs_martix.list)
>
> ======================================================================
>
>  NCS operator which transforms:
>    ( segid B ) -> ( segid A )
>
>       matrix= ( -0.44014  0.63215 -0.63770 )
>               ( -0.62202  0.29754  0.72426 )
>               (  0.64759  0.71544  0.26225 )
>       translation= (   84.76557  -49.18177   49.70381 )
>
>       rms difference=  4.29163
>
> ======================================================================
>
>  NCS operator which transforms:
>    ( segid B ) -> ( segid C )
>
>       matrix= ( -0.51502 -0.63090  0.58027 )
>               (  0.58774  0.23286  0.77482 )
>               ( -0.62395  0.74009  0.25088 )
>       translation= (  -23.52714  -79.15917   76.67988 )
>
>       rms difference=  4.10269
>
> ======================================================================
>
> -----------------------------------------------------------------
> Bernhard Rupp
> Macromolecular Crystallography and Structural Genomics
> LLNL-BBRP L448                               Phone (925) 423-3273
> University of California                     Phax  (925) 424-3130
> Livermore, CA 94551                          email    br@llnl.gov
> URL                                http://www-structure.llnl.gov
> TB Structural Genomics Consortium  http://www.doe-mbi.ucla.edu/TB
> EU Mirror         http://www.ccp14.ac.uk/ccp/web-mirrors/llnlrupp
> -----------------------------------------------------------------

--

Best Regards,

Mark

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Mark A. White, Ph.D.                                    Tel:
Sealy Center for Structural Biology                     (409) 747-4747
Dept. of Human Biological Chemistry & Genetics          Fax:
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University of Texas Medical Branch                      email:
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