Content:

• Introduction
• autoPROC
• autoSHARP

---

Introduction

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 autoproc
  module load sharp
  module load buster

After this you should be able to run

  process -h

which shows that autoPROC is configured correctly. Remember to pick up one of the reference card sheets - or get a copy here:

• autoproc_reference_card.pdf
• autosharp_reference_card.pdf
• buster_reference_card.pdf

---

autoPROC

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 should not need to download the images again - they should be 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

• decide on a directory to run in, e.g.

        mkdir /data/rapidata/John/autoPROC
        cd /data/rapidata/John/autoPROC

• on a machine to run on (see pull-up menu near the bottom of the NX session):
• open up a terminal on that machine/node
• cd into the directory you created above

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

---

autoSHARP

Using data processed with autoPROC might be the easiest here - but you could also use one of the tutorials described here.