Masking

[Eleanor Dodson <ccp4@yorvic.york.ac.uk>]

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On Jun 10,  4:07pm, Byron Delabarre wrote:
> Subject: Extending solomon output masks
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> Hello CCP4 users -
>
>
>

.....
> edit a solvent mask generated from SOLOMON to envelope what I believe is the
dimer.  As things stand, crystallographic
> contacts are obfuscating the true shape of the dimer - it is these contacts
which I am trying to edit out of the mask.
>


 This isnt quite the answer you are lookin for; but DM has the facility to do
something like this automatically.

 You ask for NCSMASK NMER 2 ( in your case)

and approximations to the matrices you think relate the two molecules, and it
will both refine the matrices, and output a likely mask where the averaging
symmetry seems to be obeyed.. You can express the starting matrices in a
variety of ways; Euler angles, polar angles O matrices etc.

 In this case we had starting matrices from the heavy atom sites, but in other
caes we have started by fitting a couple of fragments by eye into each molecule
then using LSQKAB to find the rotation and translation between them..

Example with  4 molecules
dm \
hklin  $SCRATCH/nat5_hg6-unique_dm123a.mtz \
hklout $SCRATCH/nat5_hg6-unique_dm123b.mtz \
ncsout $SCRATCH/dm1232.msk \
<< 'END'
SOLC 0.60
GRID 204 204 96
MODE SOLV HIST AVER
NCYCLE 1
COMBINE OMIT
#  Identity
NCSMASK NMER 4
AVER
OMAT
    1.000000    0.000000    0.000000
    0.000000    1.000000    0.000000
    0.000000    0.000000    1.000000
    0.000000    0.000000    0.000000
AVER REFI   -0.466047   -0.407806   -0.785149
    0.617329   -0.785577    0.041634
  142.787079  199.802139   65.990707
AVER REFI
OMAT
   -0.984715    0.143999    0.097950
    0.142785    0.345329    0.927549
    0.099747    0.927274   -0.360639
  129.659378   17.179094  -44.974537
AVER REFI
OMAT
    0.615753    0.320282   -0.719910
    0.320236   -0.936454   -0.142777
   -0.719946   -0.142615   -0.679224
   25.136415  168.113831  130.769806


LABIN FP=Fnat5 SIGFP=Snat5 PHIO=PHIDM_av_hg  FOMO=FOMDM_av_hg FREE=FreeR_flag
LABOUT PHIDM=PHIDM_av2_hg  FOMDM=FOMDM_av2_hg FCDM=FCDM2 PHICDM=PHICDM2
end
'END'
Eleanor Dodson
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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
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