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[ccp4bb]: averaging



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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
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