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
[log in to unmask] 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
>>
>
>
