CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source. CrystFEL comprises programs for indexing and integrating diffraction patterns, scaling and merging intensities, simulating patterns, calculating figures of merit for the data and visualising the results. Supporting scripts are provided to help at all stages, including importing data into CCP4 for further processing.
Reference:
T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman. "CrystFEL: a software suite for snapshot serial crystallography". J. Appl. Cryst. 45 (2012), p335–341.
doi:10.1107/S0021889812002312 — Download PDF — Article on IUCr website.
- Module Name: crystfel (see the modules page for more information)
- A small set of test data downloaded from here is available in /usr/local/apps/crystfel/example
Allocate an interactive session including 100 GB of local scratch, and run the program. Sample session working through this tutorial. The sample data is copied to local scratch, and all operations are performed on this copy to reduce I/O to the central filesystems.
[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=20g --gres=lscratch:100 salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ cd /lscratch/$SLURM_JOBID [user@cn3144 ~]$ cp -r /usr/local/apps/crystfel/example . [user@cn3144 ~]$ indexamajig -i files.list -g 5HT2B-Liu-2013.geom --peaks=hdf5 -o tutorial.stream [user@cn3144 ~]$ check-peak-detection tutorial.stream -g 5HT2B-Liu-2013.geom --int-boost=5[user@cn3144 ~]$ ....etc.... [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. crystfel.sh), which uses the input file 'crystfel.in'. For example:
#!/bin/bash module load crystfel cd /lscratch/$SLURM_JOBID cp -r /usr/local/apps/crystfel/example . cd example indexamajig -i files.list -g 5HT2B-Liu-2013.geom --peaks=hdf5 --indexing=mosflm-raw-nolatt --int-radius=3,4,5 -o tutorial.stream
Submit this job using the Slurm sbatch command.
sbatch --gres=lscratch:100 crystfel.sh
Create a swarmfile (e.g. crystfel.swarm). For example, the following swarmfile runs indexamajig on several sets of data
indexamajig -i files1.list -g AB1.geom --peaks=hdf5 --indexing=mosflm-raw-nolatt --int-radius=3,4,5 -o out1 indexamajig -i files2.list -g AB2.geom --peaks=hdf5 --indexing=mosflm-raw-nolatt --int-radius=3,4,5 -o out2 indexamajig -i files3.list -g AB3.geom --peaks=hdf5 --indexing=mosflm-raw-nolatt --int-radius=3,4,5 -o out3 [...]
Submit this job using the swarm command.
swarm -f crystfel.swarm [-g #] [-t #] --module crystfelwhere
-g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
-t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
--module crystfel | Loads the crystfel module for each subjob in the swarm |