Content:


Introduction

4EYE is a small protein determined through the SSGCID initiative (see full annotation). It was originally processed with XDS, solved using Phaser and refined with REFMAC to a resolution of 2.1A.

The commands shown below should be run in a terminal, within an empty directory. It can be useful to have two terminals (or terminal tabs) open at the same time - with one being used to run the programs and the other to look at intermediate results (while jobs are still running).


Getting all files

First we need to download the images from here using either

   wget -O 4eye.tar "http://proteindiffraction.org/data/ssgcid_data_all/4eye.tar"

or

   curl -o 4eye.tar "http://proteindiffraction.org/data/ssgcid_data_all/4eye.tar"

(depending on which command is available). Then unpack them into a newly created subdirectory using

  tar -xvf 4eye.tar
  bunzip -v 4eye/series/*.img.bz2

Finally, we should fetch the sequence for this protein using e.g.

  wget -O 4eye.seq "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=fastachain&compression=NO&structureId=4EYE&chainId=A"

or

  curl -o 4eye.seq "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=fastachain&compression=NO&structureId=4EYE&chainId=A"
 

Running autoPROC data processing

This is very easy and straightforward with

  process -I 4eye/series -d autoPROC.01 | tee autoPROC.01.lis

A summary of processing steps can be seen in file autoPROC.01/summary.html - which can be loaded into your browser e.g. via

  firefox `pwd`/autoPROC.01/summary.html

(remember to reload from time to time to see new content appended to the file while autoPROC is still running). For more help in interpreting the output see also the relevant autoPROC manual.


Running autoSHARP for structure solution and model building

The results from autoPROC can be used directly in autoSHARP via

  run_autoSHARP.sh -seq 4eye.seq -ha I -nsit 10 -wvl 1.54705 -sca 01/aimless.sca -id autoSHARP.01 | tee autoSHARP.01.lis

The full output of this autoSHARP run can be seen by loading autoSHARP.01/LISTautoSHARP.html into your browser, e.g. via

  firefox `pwd`/autoSHARP.01/LISTautoSHARP.html

In the end you should have a nearly complete model of about 550 built and sequenced residues.