Well - if the CCs are 0 then no averaging can take place.
You know you can let DM make the mask itself - are you using the GUI?
It shows you what to set..
Eleanr
[email protected] wrote:
Hi,
Thanks for reminding me checking the mask. I think their might be
something wrong with the mask, since when DM read in the mask, it says:
Number of columns, rows, sections ............... 84 74 69
Map mode ........................................ 0
Start and stop points on columns, rows, sections -53 30
80 153 -4 64
Grid sampling on x, y, z ........................ 136 260 150
Cell dimensions ................................. 135.57100
260.11200 150.20000 90.00000 101.14000 90.00000
Fast, medium, slow axes ......................... Z X Y
Minimum density ................................. 0.00000
Maximum density ................................. 0.00000
Mean density .................................... 0.00000
Rms deviation from mean density ................. 0.00000
Space-group ..................................... 4
Number of titles ................................ 1
It seems the mask is just null. However, I converted it to a map file, and
coot clearly showed the mask, so I am not sure why the null mask was found
by DM. Moreover, the NCS CCs are just 0s for the mask.
Anyway, following is my NCSMASK script I used to generate the above mask,
where XYZIN is the reorganized pdb containing only a single fixed NCS unit
(chain A). and all the operations were generated by LSQKAB with Chain A
mapped to other chains. Not sure whether there is something wrong here or
not...
ncsmask xyzin ${PDB}_A.pdb mskout ${PDB}.msk << eof
SYMM P1211
EXPAND 1.0
OVERLAP 3
AVERAGE 12
#Identical
ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
TRAN 0.0 0.0 0.0
#A>C
ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273
-0.01120 -0.05203 0.99858
TRAN 101.46837 81.74413 2.89341
#A>D
ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011
-0.00451 -0.07547 0.99714
TRAN 158.03317 36.91842 3.25853
#A>F
ROTA MATRIX -0.21272 -0.97702 0.01352 0.97675 -0.21300 -0.02424 0.02657
0.00805 0.99961
TRAN 100.69797 -81.01860 -1.71365
#A>G
ROTA MATRIX 0.61704 -0.78687 -0.01005 0.78590 0.61553 0.05899 -0.04023
-0.04429 0.99821
TRAN 32.50667 -65.76570 7.05504
#A>H
ROTA MATRIX -0.85814 -0.51116 -0.04813 -0.51290 0.85771 0.03558
0.02310 0.05522 -0.99821
TRAN 156.14981 42.23873 48.93406
#A>I
ROTA MATRIX -0.13703 -0.98975 -0.04032 -0.99048 0.13635 0.01902
-0.01332 0.04254 -0.99901
TRAN 95.97630 82.30948 52.82510
#A>J
ROTA MATRIX 0.69662 -0.71695 -0.02645 -0.71716 -0.69691 0.00230
-0.02008 0.01737 -0.99965
TRAN 25.84588 59.76286 53.68224
#A>K
ROTA MATRIX 0.99467 0.10258 -0.01072 0.10259 -0.99472 0.00088 -0.01057
-0.00197 -0.99994
TRAN 0.47215 -8.86082 52.78315
#A>L
ROTA MATRIX 0.55782 0.82946 0.02875 0.82987 -0.55793 -0.00466 0.01218
0.02646 -0.99958
TRAN 36.68436 -68.63833 49.21587
#A>M
ROTA MATRIX -0.30892 0.95102 -0.01113 0.95109 0.30890 -0.00370
-0.00008 -0.01173 -0.99993
TRAN 109.48987 -79.05550 52.39334
#A>N
ROTA MATRIX -0.93676 0.34855 -0.03147 0.34600 0.93589 0.06627 0.05255
0.05119 -0.99731
TRAN 162.32979 -29.26800 45.41564
eof
The commonest error with averaging is getting the mask wrong.
Check that the CCs after application of the averaging start at a
reasonable value - 0.3 at least and increase with each cycle ( by the
way why do ncycle 1?)
But in the end the density will not be identical, the Fobs are not
perfectly symmetric so there will be differences. The best idea is to
average (with correct matrices - I always find that takes several pases
before I get them all right - then build molecule A and refit it over
the others before starting refinement.
EleanorHailiang Zhang wrote:
Hi,
I am using the following DM script to perform a NCS averaging. I have a
fundemental question: after NCS averaging, are the density distrubitions
of different NCS unit being averaged supposed to be the same? I found
they
are different by checking FCDM/PHICDM, and maybe I am wrong somewhere...
dm NCSIN ${PDB}.msk HKLIN ${PDBALL}.mtz HKLOUT ${PDBALL}-dm.mtz \
<<dmtest
mode AVER
ncycle 1
combine PERT
scheme ALL
solc 0.6213
#Identical
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
TRAN 0.0 0.0 0.0
#A>C
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273
-0.01120 -0.05203 0.99858
TRAN 101.46837 81.74413 2.89341
#A>D
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011
-0.00451 -0.07547 0.99714
TRAN 158.03317 36.91842 3.25853
#A>F
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.21272 -0.97702 0.01352 0.97675 -0.21300 -0.02424
0.02657
0.00805 0.99961
TRAN 100.69797 -81.01860 -1.71365
#A>G
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.61704 -0.78687 -0.01005 0.78590 0.61553 0.05899
-0.04023
-0.04429 0.99821
TRAN 32.50667 -65.76570 7.05504
#A>H
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.85814 -0.51116 -0.04813 -0.51290 0.85771 0.03558
0.02310 0.05522 -0.99821
TRAN 156.14981 42.23873 48.93406
#A>I
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.13703 -0.98975 -0.04032 -0.99048 0.13635 0.01902
-0.01332 0.04254 -0.99901
TRAN 95.97630 82.30948 52.82510
#A>J
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.69662 -0.71695 -0.02645 -0.71716 -0.69691 0.00230
-0.02008 0.01737 -0.99965
TRAN 25.84588 59.76286 53.68224
#A>K
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.99467 0.10258 -0.01072 0.10259 -0.99472 0.00088
-0.01057
-0.00197 -0.99994
TRAN 0.47215 -8.86082 52.78315
#A>L
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.55782 0.82946 0.02875 0.82987 -0.55793 -0.00466
0.01218
0.02646 -0.99958
TRAN 36.68436 -68.63833 49.21587
#A>M
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.30892 0.95102 -0.01113 0.95109 0.30890 -0.00370
-0.00008 -0.01173 -0.99993
TRAN 109.48987 -79.05550 52.39334
#A>N
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.93676 0.34855 -0.03147 0.34600 0.93589 0.06627
0.05255
0.05119 -0.99731
TRAN 162.32979 -29.26800 45.41564
LABIN FP = FWT PHIO = PHIC FOMO = WCMB
LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM
END
dmtest
