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CCP4BB  August 2010

CCP4BB August 2010

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Subject:

Re: DM NCS averaging question

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Mon, 30 Aug 2010 08:40:51 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (208 lines)

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
>>
> 
> 

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