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
>
>
