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Chapter 3

The environment of SHARP/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
  (1996-1997)  Eric de La Fortelle

This section of the SHARP/autoSHARP manual introduces the user to three environments that closely interact with SHARP and autoSHARP: the CCP4 suite of programs with its associated MTZ format, the SHARP Control Panel and the Preferences page.


The CCP4 suite of programs and the MTZ format


The current version of SHARP/autoSHARP requires that you have the CCP4 suite of programs installed on each computer where SHARP/autoSHARP calculations are supposed to run. For more explanations on what CCP4 is, see the CCP4 home page at Please make sure that you always have the latest version of this suite installed on your computer - although SHARP/autoSHARP only uses a subset of programs and it might well run with older versions, all updates to SHARP/autoSHARP and/or SUSHI that involve CCP4 will be relative to the latest CCP4 release. Also make sure to follow the recommendations of fixes and patches described on the "Problems page" of CCP4.

In the CCP4 system, all crystallographic data relevant to a given problem are stored in a single multi-column binary file. The format of this binary file is called MTZ. We will only provide here a SHARP/autoSHARP-oriented summary of MTZ.

MTZ : a format for crystallographic data

Two basic rules govern MTZ files : The naming convention we use in SHARP/autoSHARP is to name the MTZ files containing the amplitude measurements <something>.data.mtz (where <something> can obviously be anything - only the file extension is important).

How to prepare MTZ files for SHARP/autoSHARP

If your data processing and scaling has been done using CCP4 tools, you already have a file in MTZ format that can directly be read by SHARP/autoSHARP. If you have a file in some other format (PHASES, SCALEPACK, d*TREK, X-PLOR/CNS etc.), it may take a few more steps to prepare an MTZ file. CCP4 provides an all-purpose converter, called F2MTZ, that will take an ASCII file and convert it into an MTZ file. The catch is, that the original ASCII file should already comply with the two main requirements listed in the previous paragraph. Another tool to convert data files into MTZ format within CCP4 is called COMBAT. For some programs there are specific conversions tools available: SCALEPACK2MTZ or DTREK2MTZ.

Note: if you are running SHARP through the autoSHARP procedure you can directly supply data in a variety of formats and the conversion to MTZ is done automatically (see autoSHARP documentation).

In addition, please note that SHARP/autoSHARP reads data only in the form of structure factor amplitudes (FMID and its associated standard deviation SMID) and anomalous differences (on amplitudes as well - DANO and its associated standard deviation SANO). Transformation from intensity data (for unique reflexions) to structure factor amplitudes and anomalous differences is usually done using the CCP4 program TRUNCATE.

Note: if you use the CCP4 program TRUNCATE you might want to also keep the column ISYM. This specifies which of either F+ or F- was measured for an acentric reflection if no anomalous data is present.

Reduction to unique Miller indices, as well as the application of scales (possibly calculated elsewhere) to the data is usually done in the CCP4 program SCALA.

Documentation for these programs can be found (if CCP4 is installed on your system) by typing 'man <name-of-program>'. If the man page is not found, you have a second chance with 'more $CDOC/<name-of-program>.doc'.

The SHARP Control Panel


The front page of the SHARP/autoSHARP interface is called the SHARP Control Panel. It is reached by connecting to the SHARP/autoSHARP server installed on one of your computers (a user name and password is required for doing that). From there, you can decide what course of action to take.

The URL for the SHARP/autoSHARP server is usually of the form http://server:8080/ (obviously the machine name and the port number (8080) can be different). The user name and password was set by the administrator when creating an account. Please note, that this is completely independent of any 'normal' login/UNIX account.

Some more details for the various hyper-links:

The Preferences Page

This leads you to the Preferences page, where you can choose some important parameters of the interface (mainly about graphics and look-and-feel).
Last modification: 31.07.2013