S. Fushinobu
分子置換したモデルの位相でマップを描くときも、面倒くさがらずに、dmをかけましょう。マップが改善します。NCSを使った場合の例を御紹介。
ここを使ったりして、正しいSolvent Contentを計算しておきましょう。正確な値より、ちょっと小さめの数字を入れるべき？
dmの出力結果から、refineされたNCS Matrixが得られます。次のサイクルには、このMatrixを使いましょう。ncsmaskとdmの両方のマトリックスを書き換えるのを忘れないように。
また、CNSにもdmをやってくれるスクリプトがあります（私は使ったことがありませんが）。参考までに。詳しくはCNSのtutorialを読んで下さい。
--------------- 1predm.sh ---------------
#!/bin/csh -f
#!Take output from Xplor into a form suitable for ccp4
#!Use this script only for the pdb files from XPLOR/CNS!!
pdbset xyzin foo.pdb \
xyzout foo_ccp4.pdb << 'eof-1'
cell 62.06 62.06 113.4 90.00 90.00 90.00
spacegroup P3221
xplor
'eof-1'
#!Generate sfs and phases from this modified map.
sfall \
HKLIN foo.mtz \
HKLOUT junk1.mtz \
XYZIN foo_ccp4.pdb << 'END-sfall'
TITLE Sfs from the model (xplor)
MODE sfcalc xyzin hklin
NOSCALE
RESOL 100.0 2.7
!SFSG 1
LABI FP=FP SIGFP=SIGFP
LABO FC=FC PHIC=PHIC
end
'END-sfall'
#scale Fc vs Fo
rstats HKLIN junk1.mtz HKLOUT junk2.mtz <<'eof-rstats'
LABIN FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC
TITLE Fc to Fo scaled
RSCB 8.0 2.7
#### === === Change them!
'eof-rstats'
#caluculation of sigmaA weight (labelled WCMB)
sigmaa hklin junk2.mtz hklout foo_siga.mtz << 'eof'
TITLE Sigmaa weighted
PARTIAL !# Option for Fo-Fc type coefficients
#ERROR
LABI FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC
LABO WCMB=WCMB DELFWT=DELWFT FWT=FWT
'eof'
rm junk1.mtz
rm junk2.mtz
exit
--------------- 1predm.sh ---------------
--------------- 2dm_ncs.sh ---------------
#! /bin/csh -f
# Make ncsmask for dm with ncs
ncsmask xyzin foo_ccp4.pdb \
mskout junk.msk << eof
RADIUS 8.0 ! Default is 3.0. Use 16.0 or so for Ca structure.
OVERLAP
SYMM P3221 ! You must define if the input is pdb.
AVER 2 ! 2 means dimer. (No. of Symm. elements.)
OMAT
1 0 0
0 1 0
0 0 1
0 0 0
OMAT
-0.38373 0.77565 0.50113
0.76997 -0.03085 0.63734
0.50981 0.63041 -0.58538
17.45613 -15.93883 1.91314
eof
# density modification - Ref. Omit mode and multires calc.
# This scheme is best now (dm 2.0) for dm with NCS averaging
# without phase extension. (Phase extention is dm calculation for
# higher resolition determined/refined before.)
# Check the resolution of the mtz file if it does not exceed
# the resolution used before.
# You can get refined ncs matrix from output.
# You MUST see the "man dm" output to get the best result.
# by S.Fushinobu
dm hklin foo_siga.mtz \
hklout foo_dm.mtz \
ncsin1 junk.msk<< 'my-data'
SOLC 0.57
#### ==== Change This!
MODE SOLV HIST MULT AVER
COMBINE PERT
NCYCLE 20
!SCHEME ALL ! no need to define for dm without phase extention.
AVER REFI ! You can get refined ncs matrix
OMAT
1 0 0
0 1 0
0 0 1
0 0 0
AVER REFI ! Define for each Symm. Ops?
OMAT
-0.38373 0.77565 0.50113
0.76997 -0.03085 0.63734
0.50981 0.63041 -0.58538
17.45613 -15.93883 1.91314
LABIN FP=FP SIGFP=SIGFP -
PHIO=PHIC FOMO=WCMB
LABOUT FDM=FDM1 PHIDM=PHIDM1 FOMDM=FOMDM1
END
'my-data'
rm junk.msk
exit
--------------- 2dm_ncs.sh ---------------
--------------- 3mapmake.sh ---------------
#! /bin/csh -f
#!Calculate map.
fft HKLIN foo_dm.mtz \
mapout junk1.map << 'END'
RESOL 6.0 2.7
##### === === Change This!
SCALE F1 2.0 0.0 F2 1.0 0.0
#FFTSPACEGROUP 1 # This makes true space group for your SG?
TITLE 2Fo-Fc map after dm
XYZLIM 0 1.0 0 1.0 0 1.0
#BINMAPOUT21
LABI F1=FP SIG1=SIGFP PHI=PHIDM1 F2=FC SIG2=SIGFP W=FOMDM1
'END'
###################################################################
# Extend the difference map to cover the molecule + 4 Ang
###################################################################
mapmask mapin junk1.map mapout junk2.map \
xyzin foo_ccp4.pdb <<eof-mapmask
border 4
mode mapin
eof-mapmask
/usr/xtal/gerard/bin/6d_mapman -b <<eof
read m1 junk2.map ccp4
norm m1
mappage m1 foo_dm.omap
quit
eof
rm junk1.map
rm junk2.map
exit
--------------- 3mapmake.sh ---------------