TutorialCcp4Dls2017

Content:

• Introduction
• Setup
• Example datasets and tutorials

Introduction

Here we will collect some information regarding use of our software (during tutorials or when using it on your own) that is particular to the setup during the DLS-CCP4 Data Collection and Structure Solution Workshop November (30th - December 7th 2017).

We will try and keep this page here up-to-date as we get settled in during the running of the course.

Setup

You might need to load a so-called module (every time you open a shell/terminal):

% module load ccp4-workshop
% module load sharp

Notes:

• the first command might take a long time when run for the first time: it also copies over a lot of tutorial/example data
• this needs to be run every time you open a new terminal
• you will also be "placed" into a working directory - you could/should make a note of this via

       pwd

• the last command might not be necessary (since the first command should setup everything in one go)
• similarly for BUSTER ("module load buster") and autoPROC ("module load autoPROC").

There are different ways of running autoSHARP:

• From within the CCP4i (not yet in CCP4i2) there is an autoSHARP task in

      Experimental Phasing
        --> Automated Search & Phasing
              --> autoSHARP

• This might have the advantage of presenting a familiar interface for users familiar with CCP4.
• However, looking at resulting maps and models requires a bit more work (one needs to download/save files first before loading them into Coot).
• When loading MTZ files from SHARP/autoSHARP into Coot you need to select the correct columns for the type of map you want to look at (see here for details if the column naming is not already obvious).
• Please ensure that you have configured CCP4i correctly to use your browser of choice (e.g. firefox) as so-called "hypertext" viewer.
• If someone is interested in contributing an autoSHARP interface for CCP4i2: please let us know!

• If you can type "run_autoSHARP.sh -h" in a terminal (and it comes back with the help message), then everything should be setup correctly for using the command-line interface to autoSHARP. You might want to have a printout of the autosharp_reference_card.pdf handy to help with usage.

• Be sure to be roughly familiar with Unix command line (terminal/shell). See e.g. some online tutorials:
• http://www.ee.surrey.ac.uk/Teaching/Unix/unixintro.html
• http://linuxcommand.org/learning_the_shell.php

• This interface has the advantage of creating (at the end) little scripts to present results from various stages of structure solution easily within Coot - see the messages written to standard output. You can run those using e.g.

          % coot --script 04_coot.scm
 

Example datasets and tutorials

Please see the general page with examples and tutorials:

• Try and pick a run that is likely to be fast - this will give you a good overview over all aspects of experimental phasing via SHARP/autoSHARP. You could pick one of the SAD examples - or try using a single wavelength of the faster running MAD examples.

• Or use your own data, especially if you have
• a sequence file (see here for format description)
• one or more reflection file(s) (ideally a merged *.sca file, e.g. from running autoPROC)
• information about heavy atom(s) (number, f'/f'' etc)