[Chimera-users] Precomputing subsampled map sizes

Thomas Goddard goddard at cgl.ucsf.edu
Tue Jan 30 15:20:51 PST 2007

Hi Jeff,

   Yes, Chimera will complain and not allow precomputed volume 
subsamples if the size of the subsample grid is not what is expected.

   In the case you give (1434,1434,110) with subsample grid of size 
(358,358,26) the subsample grid size is not acceptable.  Notice that 4 
times the subsample size is (1432, 1432, 104)  So a half size bins in 
the first two dimensions are left off (1434 - 1432 = 2) -- that is fine. 
  But the third dimension is missing 1.5 bins (110 - 104 = 6).  The 
subsample file should have size 27 in the third dimension, ie 
(358,358,27).  I don't know why squeezevol from IMOD dropped off more 
than a whole bin in the third dimension.  Chimera allows fractional bins 
to be dropped off, but does not allow whole bins to be missing.


Jeff wrote:
> hi again,
> is there a problem with the precomputed subsamplings needing even 
> dimensions (I pre-cut my volume to even dimensions so that a binning of 
> 2 would result in a whole number for the subsampled dimensions, but it 
> can be hard to do this for a factor of 8 in advance).
> chimera is complaining to me about bad dimensions ('Data foo.mrc of size 
> (358,358,26) not a valid size for dubsamples of foo.mrc of size 
> (1434,1434,110).
> is there a program you use to bin / get around this problem? I use 
> 'squeezevol' from IMOD, I am not sure if it is completely transparent in 
> its output for what chimera would expect
> -j

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