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Chapter 1

Short introduction to autoSHARP

Copyright    © 2001-2006 by Global Phasing Limited
  All rights reserved.
  This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL.
Documentation    (2001-2006)  Clemens Vonrhein

This manual will give a very short overview and some general remarks about autoSHARP. However, although it should help you getting started it might be a good idea to browse the full manual - maybe while the job is running?


What you need

  1. data file(s) in MTZ, SCALEPACK or SHELX format

  2. molecular weight (in Dalton), number of residues or ideally a sequence file of what's in the asymmetric unit

  3. wavelength(s) (in Å) and/or ideally f'/f" values (e.g. from a fluorescence scan)

  4. a rough idea about the number and atomic type of the "heavy atoms" in your crystal(s)

  5. if you already know the positions of your heavy atoms: a file containing coordinates.


All files that you want to use with autoSHARP have to be in your sharpfiles/datafiles directory (which is usually a subdirectory of your home directory). They need to be readable by the server. The various files are recognised by their file extension:

Only after you have copied all necessary files to these locations will they be visible in your browser (you might need to press the "Reload" button). Also make sure that the permissions on these files is correct:

% chmod 0644 somefile

If you feel the need for other file formats to be implemented - please feel free to get in contact with us (best with an example file attached to your email).


Specifying the necessary input information is a two step procedure:
  1. specify type of experiment, number of data sets(e.g. MAD with 3 wavelengths or SIR(AS) with 1 derivative) special types of datasets and speed/accuracy settings.
  2. give detailed information about each data set and the general problem.

These input forms are started from the main SHARP Control Panel. You can either start autoSHARP based on a previous run (e.g. if you just want to change a few parameters) or from scratch (i.e. based on "None").

Once you submit the job you can look at the results through one main HTML document (called LISTautoSHARP.html). You need to hit the "Reload" button on your browser from time to time to get the latest version of this document. From this document you can see more details about the various steps performed through the "details" link. This will present another HTML document that (finally) will contain a table of contents at the top, all important information and further links to the detailed output of various programs. Again, you need to hit "Reload" from time to time.

Each autoSHARP job is started in its own subdirectory within your sharpfiles/logfiles directory structure. This subdirectory will contain the main LISTautoSHARP.html file.If you requested to do heavy atom refinement and phasing, at least one additional subdirectory will be created (again, within your sharpfiles/logfiles directory structure and with the run number incremented by one). This will contain a LIST.html file of the first SHARP run (heavy atom refinement and phasing). If the automated checking of the various residual maps didn't result in the addition or deletion of heavy atom sites after the first SHARP run, only one additional (phasing only) SHARP run is necessary to get phases in the inverted hand. If, however, additional heavy atom sites were detected (or wrong heavy atom sites removed) one further refinement and phasing run of SHARP is done for the original hand.

So you can end up with a directory structure like this:

  sharpfiles/logfiles/<identifier><run>    -> LISTautoSHARP.html
                      <identifier><run+1>  -> first SHARP run:
                                              initial; refinement and phasing
                      <identifier><run+2>  -> second SHARP run:
                                              further refinement or
                                              inverted hand phasing
                      <identifier><run+3>  -> last SHARP run:
                                              inverted hand phasing if necessary
Note: the last but one SHARP run (referred to as "original" hand) and the last SHARP run ("inverted" hand) will have the same heavy atom model (apart from the inversion of coordinates).

Anyway, all the necessary files/directories are available through the main LISTautoSHARP.html file.

Last modification: 25.07.06