Content:
We assume that you are already connected via NX to the rapidata account for this course - and that you have selected a compute node from the pull-down menu. You might want to open two terminals this way: one for running jobs and one for looking at results along the way.
If
process -h
returns an error you will need to setup your environment for running autoPROC (and the other programs from Global Phasing):
module load ccp4/7.0 module load xds module load autoproc module load sharp module load buster
After this you should be able to run
process -h
which shows that autoPROC is configured correctly.
If you don't have your own data available for processing, you can use the example datasets described here. These include several SAD, MAD and SIR examples. You will not need to download the images again: they are already available on disk at:
/data/rapidata/PublicData/4E0E /data/rapidata/PublicData/4EYE /data/rapidata/PublicData/5BP7 /data/rapidata/PublicData/5BXG /data/rapidata/PublicData/4U4H/140 /data/rapidata/PublicData/4U4H/141
Before running a tutorial, you need to
mkdir /data/rapidata/John/autoPROC cd /data/rapidata/John/autoPROC
So any of the tutorials could be run with commands like
process -I /data/rapidata/PublicData/XYZ ... -d 01 | tee 01.lis
(to run the actual job) and in a second terminal
firefox 01/summary.html
to visualise the results as they are coming in (don't forget to reload that page from time to time).
For subsequent autoSHARP runs you want to use the files
ls -l 01/*.sca
Using data processed with autoPROC might be the easiest here - but you could also pick up the reflection files directly from
/data/rapidata/PublicData/4E0E/4e0e.seq /data/rapidata/PublicData/4E0E/autoPROC_4e0e_hrem.sca /data/rapidata/PublicData/4E0E/autoPROC_4e0e_infl.sca /data/rapidata/PublicData/4EYE/4eye.seq /data/rapidata/PublicData/4EYE/autoPROC_4eye.sca /data/rapidata/PublicData/4U4H/4u4h.seq /data/rapidata/PublicData/4U4H/autoPROC_4uh4_hg.sca /data/rapidata/PublicData/4U4H/autoPROC_4uh4_nat.sca /data/rapidata/PublicData/5BP7/5bp7.seq /data/rapidata/PublicData/5BP7/autoPROC_5bp7.sca /data/rapidata/PublicData/5BXG/5bxg.seq /data/rapidata/PublicData/5BXG/autoPROC_5bxg.sca
With these datasets you should be able to follow the tutorials described here.