Ten Years and Change the MX data archive at ALS 8.3.1.

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Presentation transcript:

Ten Years and Change the MX data archive at ALS 8.3.1

ALS data collection history terabytes (uncompressed)

ALS data collection history terabytes (uncompressed)

ALS data collection history images x 10 6

ALS data collection history images x 10 6

ALS data collection history images x PDB entries

ALS data collection history images x PDB entries

images x PDB entries

DVD data archive: 82 TB

Which data go with which PDB? 260,000 images are called “test” cell: – is within 5 Å and 5° of 16,000 PDBs focusing on PDBs credit ALS with data 44 of these didn’t actually collect data 64 collected data, but no credit

1.images from collected “near” edges 3.find “runs” of >10 images 4.unify multi-wedge sets 5.run labelit & XDS 6.>70% complete? 7.I/σ > 10 8.reduced cell vs PDB 1,604, , to 200+ Which data go with which PDB?

Responses to inquiries “I have to find my old note book as I have no idea what that is.” “I have changed jobs a few times since and am really far away from crystallography now.” “Will see what I can find.” “We solved it but never published it. Sorry!”

DVD data archive

Primary failure mode of DVDs

dataset identification protocol 1.images from collected “near” edges 3.find “runs” of >10 images 4.sort out multi-wedge sets 5.run XDS 6.>70% complete? 7.I/σ > 10 8.reduced cell vs PDB 1,604, , to 200+

Unit Cell: best R cryst after rigid-body refinement RMS unit cell length deviation (Å) 1hh7 M. TB CSOR 1rb5 myoglobin

MAD/SAD datasets R iso vs PDB deposit best R cryst after rigid-body refinement Published non-isomorphous Unsolved?

EGDA Dec 01 19:45: egda46_*1_E#_###.img (1112 images, Se MAD) Dec 02 15:10: egda27_*1_###.img (180, 1A, native?) Dec 02 19:21: egdau1_*1_###.img (427, 8000eV (U?) SAD) Dec 02 20:58: egdau1_*2_###.img (360, 8000eV (U?) SAD) Jun 01 14:07: egda60_*1_###.img (360, Lutetium SAD) “I think that these EGDA data sets are very likely some of xxx’s data sets, he was working on E.coli guanine deaminase, something he brought from yyy. No structure was ever published James, xxx was unable to solve the structure from these data.”

~2.9 Å P R = 0.32 R free = 0.39 PDB ID: ???? E. coli guanine deaminase

Summary saving data could double productivity unit cell is not a good score lossy compression: rallying cry? backup vs archive metadata: what do we really know?

Brief Summary this is a lot of work. who is going to pay for it?

backblaze.com “pod” server backblaze.com offers “unlimited storage” data backup for $5/month.

backblaze offers “unlimited storage” data backup for $5/month.

backblaze does not sell these “pods”, but “protocase.com” will.

compresses 4.2x

compresses 337x

compresses 5x, but only one per dataset!

compresses 3.5x

compressed ~50x

compresses 5.2x

Lossy compression vs R/R free R factor compression ratio