How to use SHARP under UNIX

Note : we highly recommend running the various programs through the interface - at least to get started and to make sure the whole installation is correct. Furthermore, if you run the programs outside the interface, various links will be setup differently, and you might not be able to view some results through the external viewers provided with Sushi.

Contents

• Introduction
• Running SHARP
• Running autoSHARP
• Running solvent flattening
• Running automatic building

Introduction

You also need to know the architecture you're running on. Currently, the following architectures are available:

Name	Description
irixn32	IRIX (6.2 and later)
alpha	Digitial Unix / Tru64 Unix (Compaq/HP)
linux	Intel/Linux

We will assume, that you want to keep all files and results within the sharpfiles directory structure. This way it is still possible to view and maintain results through the interface. However, you can also run the various programs in any directory. As an example, lets assume your project is called "Lysozyme-MAD-X31" and you're starting with the first run.

The following examples are all given as Bourne shell (sh): they should also be correct for shells like bash or ksh. You can easily change them to csh or tcsh syntax.

Running SHARP

1. Preparation :

   You need to get a few files/links into place. This is done by creating a directory Lysozyme-MAD-X31.1 (e.g. in ~/sharpfile/logfiles). Inside this new directory, create the following files/links:

   • SIN : SHARP input file (see syntax). You could prepare this via the interface - or take another SIN file as example and edit it according to your experiment.

   • edit the SIN file and change the value of the DATAFILES and OBSFILE keywords. This is the recommended way.

     Please note that from SHARP 2.0.0 onwards, the OBSFILE keyword is located in the general (top) section of the SIN file. However, for backwards compatibility to previous SHARP versions, the older syntax (with it being defined at the BATCH level) is still supported.

     Alternatively, create a file with name REFL01.mtz : this is the MTZ reflection file SHARP is using. It should contain all the columns referenced in the SIN file. If this file is present in the current directory, SHARP will use this instead of the values given in the SIN file via the DATAFILES/OBSFILE keywords..

2. Running it :

   Use the following small script as an example and run it within the newly created Lysozyme-MAD-X31.1directory:

   #!/bin/sh # set BDG_home: BDG_home=/where/ever/sharp # define SHARP binary: EXE=$BDG_home/bin/alpha_exe/sharp # these should be there: SYMOP=$BDG_home/database/symop ATOMSF=$BDG_home/database/atomsf export BDG_home SYMOP ATOMSF $EXE > LIST.html 2> STDERR

Running autoSHARP

1. Preparation :

   You need to prepare a directory and an input file. This is done by creating a directory Lysozyme-MAD-X31.1 (e.g. in ~/sharpfile/logfiles). Inside this new directory, create the following file:

   • .autoSHARP : autoSHARP input file. You should prepare this via the interface - or take another *.asin file as example and edit it according to your experiment.

   Make sure that all files referenced in this .autoSHARP file are located in the current directory. See the list of supported files.

2. Running it :

   Use the following small script as an example and run it within the newly created Lysozyme-MAD-X31.1directory:

   #!/bin/sh # set BDG_home: BDG_home=/where/ever/sharp # command (this should be there): CMD=$BDG_home/bin/sharp/detect.sh export BDG_home $CMD > LISTautoSHARP.html 2>&1

Running solvent flattening

1. Preparation :

   You need to prepare a directory and an input file. This is done by creating a subdirectory solo_50.0pc within your Lysozyme-MAD-X31.1 directory (which is in ~/sharpfile/logfiles). Additionally, create the following file:

   • .sharprc : phase improvement and interpretation control file. You should prepare this via the interface - or take an old file as example and edit it according to your experiment.

2. Running it :

   Use the following small script as an example and run it within the Lysozyme-MAD-X31.1 directory:

   #!/bin/sh BDG_home=/where/ever/sharp CMD=$BDG_home/bin/sharp/solomon.sh export BDG_home $CMD > solo_50.0pc.log.html 2>&1

Running automatic building

1. Preparation :

   You need to prepare a directory and an input file. This is done by creating a subdirectory wARP_50.0pc within your Lysozyme-MAD-X31.1 directory (which is in ~/sharpfile/logfiles). Inside this new directory, create the following files:

   • warp.par : ARP/wARP parameter file. You could prepare this via the interface, take an old file as example and edit it according to your experiment or use the original ARP/wARP tools to prepare it. It should be a standard ARP/wARP (version 5.1) parameter file.

   • .arpwarp : a special parameter file for the (slightly modified) ARP/wARP "warpNtrace" script we usually use. Take an old file as an example.

2. Running it :

   Use the following small script as an example and run it within the Lysozyme-MAD-X31.1/wARP_50.0pc directory:

   #!/bin/sh BDG_X="sharp" BDG_home=/where/ever/sharp CMD=$BDG_home/bin/sharp/arpwarp.sh export BDG_home . $BDG_home/.bdgrc $CMD > ../wARP_50.0pc.log.html 2>&1