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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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