radiation damage series?

[mysecondnameisdanger]

How to treat radiation damage series?
Let's say I collected the same dataset from the same crystal many times...(each time with 2 sweeps, defined in the master.h5 file).

I am doing a simple for loop in bash like this ..

#!/bin/bash
# First crystal
for i in `seq -w 49 72`
do
  mkdir ${i}
  # run xia2 in the folder with the datasets
  xia2 pipeline=dials space_group=X /home/msnid/NSLS2/${i} image=/home/msnid/NSLS2/Test-msnid-3-15_122${i}_master.h5
done

Is this the correct way to do it?

[graeme-winter]

You have two sweeps in each master file?

TBH for this use case I would use "raw" DIALS

dials.import /home/msnid/NSLS2/Test-msnid-3-15_122??_master.h5
dials.find_spots imported.expt
dials.index imported.expt strong.refl [space_group=X if you think it would help]
dials.refine indexed.expt indexed.refl
dials.integrate refined.expt refined.refl
dials.symmetry integrated.expt integrated.refl
dials.scale symmetrized.expt symmetrized.refl \
  anomalous=true absorption_level=medium

or something similar, then look at the output from the scaling to see how the sample evolved over time. This does depend on the two sweeps being correctly understood geometry wise, as it only indexes all N sweeps with a single orientation matrix to start with, but ensures in scaling that these all have the same unique Miller index

I'll keep this issue open and close the one in xia2

[dagewa]

Possibly relevant: cctbx/dxtbx#13

[mysecondnameisdanger]

uhmmm
... sorry...for the confusion...
I have two masters (one for each sweep). Each master with two data (*_data_00000?.h5) files.

I was asking because, I believe (Am I right?) I need to specify the first dataset as a reference for all later datasets? (I am planning to run ridl later)

Strangely enough (or at least I was not expecting it), xia2 can run only 1 sweep. (specifying one master only), should not this print a warning or something?

Thanks...

[graeme-winter]

If each master.h5 has > 1 data file that's no problem at all

You have many master.h5 files taken one after the other on the same crystal? Then the spell above will work fine

[mysecondnameisdanger]

I have

Test-msnid-3-15_12249_data_000001.h5
Test-msnid-3-15_12249_data_000002.h5
Test-msnid-3-15_12249_master.h5
Test-msnid-3-15_12250_data_000001.h5
Test-msnid-3-15_12250_data_000002.h5
Test-msnid-3-15_12250_master.h5
Test-msnid-3-15_12251_data_000001.h5
Test-msnid-3-15_12251_data_000002.h5
Test-msnid-3-15_12251_master.h5
Test-msnid-3-15_12252_data_000001.h5
Test-msnid-3-15_12252_data_000002.h5
Test-msnid-3-15_12252_master.h5
Test-msnid-3-15_12253_data_000001.h5
Test-msnid-3-15_12253_data_000002.h5
Test-msnid-3-15_12253_master.h5
Test-msnid-3-15_12254_data_000001.h5
Test-msnid-3-15_12254_data_000002.h5
Test-msnid-3-15_12254_master.h5
Test-msnid-3-15_12255_data_000001.h5
Test-msnid-3-15_12255_data_000002.h5
Test-msnid-3-15_12255_master.h5
Test-msnid-3-15_12256_data_000001.h5
Test-msnid-3-15_12256_data_000002.h5
Test-msnid-3-15_12256_master.h5
Test-msnid-3-15_12257_data_000001.h5
Test-msnid-3-15_12257_data_000002.h5
Test-msnid-3-15_12257_master.h5
Test-msnid-3-15_12258_data_000001.h5
Test-msnid-3-15_12258_data_000002.h5
Test-msnid-3-15_12258_master.h5
Test-msnid-3-15_12259_data_000001.h5
Test-msnid-3-15_12259_data_000002.h5
Test-msnid-3-15_12259_master.h5
Test-msnid-3-15_12260_data_000001.h5
Test-msnid-3-15_12260_data_000002.h5
Test-msnid-3-15_12260_master.h5
Test-msnid-3-15_12261_data_000001.h5
Test-msnid-3-15_12261_data_000002.h5
Test-msnid-3-15_12261_master.h5
Test-msnid-3-15_12262_data_000001.h5
Test-msnid-3-15_12262_data_000002.h5
Test-msnid-3-15_12262_master.h5
Test-msnid-3-15_12263_data_000001.h5
Test-msnid-3-15_12263_data_000002.h5
Test-msnid-3-15_12263_master.h5
Test-msnid-3-15_12264_data_000001.h5
Test-msnid-3-15_12264_data_000002.h5
Test-msnid-3-15_12264_master.h5
Test-msnid-3-15_12265_data_000001.h5
Test-msnid-3-15_12265_data_000002.h5
Test-msnid-3-15_12265_master.h5
Test-msnid-3-15_12266_data_000001.h5
Test-msnid-3-15_12266_data_000002.h5
Test-msnid-3-15_12266_master.h5
Test-msnid-3-15_12267_data_000001.h5
Test-msnid-3-15_12267_data_000002.h5
Test-msnid-3-15_12267_master.h5
Test-msnid-3-15_12268_data_000001.h5
Test-msnid-3-15_12268_data_000002.h5
Test-msnid-3-15_12268_master.h5
Test-msnid-3-15_12269_data_000001.h5
Test-msnid-3-15_12269_data_000002.h5
Test-msnid-3-15_12269_master.h5
Test-msnid-3-15_12270_data_000001.h5
Test-msnid-3-15_12270_data_000002.h5
Test-msnid-3-15_12270_master.h5
Test-msnid-3-15_12271_data_000001.h5
Test-msnid-3-15_12271_data_000002.h5
Test-msnid-3-15_12271_master.h5
Test-msnid-3-15_12272_data_000001.h5
Test-msnid-3-15_12272_data_000002.h5
Test-msnid-3-15_12272_master.h5
Test-msnid-3-16_12273_data_000001.h5
Test-msnid-3-16_12273_data_000002.h5
Test-msnid-3-16_12273_master.h5
Test-msnid-3-16_12274_data_000001.h5
Test-msnid-3-16_12274_data_000002.h5
Test-msnid-3-16_12274_master.h5
Test-msnid-3-16_12275_data_000001.h5
Test-msnid-3-16_12275_data_000002.h5
Test-msnid-3-16_12275_master.h5
Test-msnid-3-16_12276_data_000001.h5
Test-msnid-3-16_12276_data_000002.h5
Test-msnid-3-16_12276_master.h5
Test-msnid-3-16_12277_data_000001.h5
Test-msnid-3-16_12277_data_000002.h5
Test-msnid-3-16_12277_master.h5
Test-msnid-3-16_12278_data_000001.h5
Test-msnid-3-16_12278_data_000002.h5
Test-msnid-3-16_12278_master.h5
Test-msnid-3-16_12279_data_000001.h5
Test-msnid-3-16_12279_data_000002.h5
Test-msnid-3-16_12279_master.h5
Test-msnid-3-16_12280_data_000001.h5
Test-msnid-3-16_12280_data_000002.h5
Test-msnid-3-16_12280_master.h5
Test-msnid-3-16_12281_data_000001.h5
Test-msnid-3-16_12281_data_000002.h5
Test-msnid-3-16_12281_master.h5
Test-msnid-3-16_12282_data_000001.h5
Test-msnid-3-16_12282_data_000002.h5
Test-msnid-3-16_12282_master.h5
Test-msnid-3-16_12283_data_000001.h5
Test-msnid-3-16_12283_data_000002.h5
Test-msnid-3-16_12283_master.h5
Test-msnid-3-16_12284_data_000001.h5
Test-msnid-3-16_12284_data_000002.h5
Test-msnid-3-16_12284_master.h5
Test-msnid-3-16_12285_data_000001.h5
Test-msnid-3-16_12285_data_000002.h5
Test-msnid-3-16_12285_master.h5
Test-msnid-3-16_12286_data_000001.h5
Test-msnid-3-16_12286_data_000002.h5
Test-msnid-3-16_12286_master.h5
Test-msnid-3-16_12287_data_000001.h5
Test-msnid-3-16_12287_data_000002.h5
Test-msnid-3-16_12287_master.h5
Test-msnid-3-16_12288_data_000001.h5
Test-msnid-3-16_12288_data_000002.h5
Test-msnid-3-16_12288_master.h5
Test-msnid-3-16_12289_data_000001.h5
Test-msnid-3-16_12289_data_000002.h5
Test-msnid-3-16_12289_master.h5
Test-msnid-3-16_12290_data_000001.h5
Test-msnid-3-16_12290_data_000002.h5
Test-msnid-3-16_12290_master.h5
Test-msnid-3-16_12291_data_000001.h5
Test-msnid-3-16_12291_data_000002.h5
Test-msnid-3-16_12291_master.h5
Test-msnid-3-16_12292_data_000001.h5
Test-msnid-3-16_12292_data_000002.h5
Test-msnid-3-16_12292_master.h5
Test-msnid-3-16_12293_data_000001.h5
Test-msnid-3-16_12293_data_000002.h5
Test-msnid-3-16_12293_master.h5
Test-msnid-3-16_12294_data_000001.h5
Test-msnid-3-16_12294_data_000002.h5
Test-msnid-3-16_12294_master.h5
Test-msnid-3-16_12295_data_000001.h5
Test-msnid-3-16_12295_data_000002.h5
Test-msnid-3-16_12295_master.h5
Test-msnid-3-16_12296_data_000001.h5
Test-msnid-3-16_12296_data_000002.h5
Test-msnid-3-16_12296_master.h5

what spell? your spell (dials/raw) or my spell (xia2/dials)?