[chimera-dev] big volume data

[Tom Goddard]

Hi Matt,

You should be able to just open the 80 Gbyte file.  Chimera will choose an initial subsampling and only read the part of the data it needs, so your computer does not need to have a lot of memory.  To show a subregion at higher resolution you can use volume viewer menu Features / Subregion Selection to drag a box and crop.  Volume viewer automatically adjusts the subsampling according to the “Adjust step…” setting menu Features / Data Display Options.  If the idea is that you simply want to zoom in and have it automatically crop around the center of view say and reduce subsampling — no it doesn’t do that.  It could but performance would be slow as it reads new higher resolution data so it wouldn’t be very interactive.  In order to get the best performance you want the large data saved in a file at multiple resolutions — only the Chimera map format *.cmap does that.  I think you can open the file then use volume viewer Save Map As… and save it in *.cmap format and Chimera is smart enough to not try to read the whole file into memory, but will copy it to the new format 1 plane at a time (including subsampling).  Not sure if I remember that correctly though.

	Tom


> On Jun 3, 2016, at 1:57 PM, Dougherty, Matthew T wrote:
> 
> I have a 80GB tomogram.  Is there a way to read it into chimera, such as the chimera map format & chunking, or some multiscale feature?
> 
> Viewing entire volume at low resolution subsampling as a starting point, then be able to zoom into a ROI for maximum resolution is desired.
> 
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine
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