The environment of SHARP/autoSHARP

Contents

• The CCP4 suite of programs and the MTZ format
  • Introduction
  • MTZ :a format for crystallographic data
  • How to prepare MTZ files for SHARP/autoSHARP
• The SHARP Control Panel
  • Introduction
  • Help
  • Documentation
  • Tutorials
  • Change password
  • Preferences
  • Start
  • Request
  • Examine
  • Delete
  • Browse
  • About
  • Mail
• The Preferences page
  • User level
  • Job submission scheme
  • General layout of maps
  • Display
  • Display viewer
  • Peak picking
  • Skeletonisation
  • Objects
  • Results options
  • Output options

The CCP4 suite of programs and the MTZ format

Introduction

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

• Miller indices represent unique reflexions under all symmetry operations in reciprocal space, including Friedel symmetry. A direct consequence is that the anomalous difference, if it exists, is an attribute of this unique indices (h,k,l).
• All information pertaining to a unique set of Miller indices (h,k,l) is found in one MTZ file. If you need to add information, you add columns to that file. Utility programs are provided in the CCP4 installation.

How to prepare MTZ files for SHARP/autoSHARP

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

Introduction

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:

• Help : describes the SHARP Control Panel (ie this document)

• Documentation : leads you to all installed documentation (including this document)

• Tutorials : leads you to the installed set of example datasets and tutorials

• Change password : is used to change your password for using the SHARP server. After you change your password, you will be asked to re-authenticate again. Additionally, you might get asked for your password again if you first connected to http://server:8080/ (host name alias) but then you are linked to e.g. http://server.domain.com:8080/ (full host name).

• Preferences : leads you to the Preferences page where you can change various settings.

• Start : buttons are provided for running SHARP or the automated procedure autoSHARP. These will give you an input form (or several) where you can fill in the necessary information for the particular task.

  On the right hand side of these buttons you can see a menu of previous inputs, including probably the tutorials that we supply with the release. You may use the parameters of a previous calculation as a template for the parameters of your present crystallographic problem. Or start with a form filled with default values by selecting 'None'. In these pages, you will find context-sensitive help by clicking on highlighted words or expressions.

• Request : is used to perform an action on a running calculation. The type of action is selected in the menu immediately to the right, and the calculation name is selected in the next menu on the right.

  The types of actions are :

  • Nothing : the default. No action taken.
  • Shutdown : stop the calculation as soon as possible (SHARP and autoSHARP).
  • Restart : restart a calculation from its initial parameters (SHARP).
  • Stop at end of current cycle : stop the calculation at the end of the current BIG cycle (SHARP).

• Examine : is used to view results as well as cardfiles, datafiles, and logfiles.
  • results will present a simple overview of all jobs so far, ordered by name, size or date. This is the easiest way to go directly to the latest runs and find your way through the output.
  • cardfiles are the input instructions to SHARP (also called SIN files - file extension *.sin) and autoSHARP (with file extension *.asin)
  • datafiles are all other input files used by SHARP and autoSHARP, such as (partial) models, observed data, sequences, known heavy atom sites etc
  • logfiles are result directories produced by SHARP (one per run) and autoSHARP (one or several per run)

• Delete : the page displayed is used to remove both cardfiles and logfiles from disk, for a given run. Attention: these results tend to accumulate, especially when you start using SHARP/autoSHARP and make a few mistakes. Do not forget to 'clean up' from time to time, using this facility.

• Browse : is used to look at various documents relevant to SHARP and autoSHARP.

• About : for finding out more about this page, and about the BUSTER Development Group (Gérard Bricogne's group at Global Phasing Ltd, Cambridge, developing SHARP/autoSHARP and BUSTER-TNT).

• Mail : is used for sending mail to the SHARP discussion group (you need to be subscribed to this group for this), the site administrator (set locally as the person responsible for the SHARP/autoSHARP installation - please ensure that this account is mail-capable), and the developers of SHARP/autoSHARP (to report bugs directly to us, but we strongly advise you to report bugs to the SHARP site administrator first).

The Preferences Page

• User level : If you think you understand SHARP/autoSHARP well, and wish to do unconventional things, you can try becoming "ADVANCED" or "EXPERT". But we advise you not to do so until the multiple security and fool-proofing checks done at "STANDARD" level get in your way.

• Job submission scheme : Here you can define the default way of submitting your various jobs. Usually, your SHARP site administrator configured one or more ways of submitting jobs. You can still change it each time you actually going to submit the job though.

• General layout of maps

  Several types of map are available:

  • Electron density : ordinary electron density maps, calculated after heavy atom refinement and phasing with SHARP.
  • Heavy atom model : when looking at residual maps, a map of your current heavy atom model is included.
  • Residual :after heavy atom refinement with SHARP you can look at various types of residual maps that help you identify additional or minor heavy atom sites or to generally correct your current heavy atom model.
  • Solvent flattened map : after phase improvement and (optionally) phase extension this is the density modified map.
  • ARP/wARP map : if you performed some automatic model building with ARP/wARP this is the map you're going to look at.

  For each map you can specify several things:

  • Pick peaks : if you want to pick peaks in this map - only really sensible in residual maps.
  • Number of contours : the number of contour levels to use. A maximum of 3 can be given.
  • Contour values : for each of the specified number of contours you can give the specific level. This can be either positive or negative. The default values should be adequate.
  • [rms] : to specify if the values given for the contour levels are in absolute units or in units of the root-mean-square (rms) of the map.
  • Colours : for each contour level you can specify the colour it should be shown with. We're using some "meta" names for various colours to have a similar look-and-feel for various graphics programs.

• Display : you can set the default region that you want to display maps in (asymmetric unit, whole unit cell or around a specified PDB file). If contouring around a PDB file the specified radius will be used.

  We currently mainly support O as an external program for viewing maps and models. Alternatively, you can always save the various maps as a tar file containing all maps in standard CCP4 format.

• Peak picking : for maps in which you want to pick peaks in (see above) as well as for general peak picking tools you can specify the cutoff level and the number of peaks you want to pick. The cutoff level is given in rms units: if a negative value is given we will pick peaks below this value and above the abs(value). This way you can see all relevant significant peaks in your map.

• Objects : various non-map objects are displayed together with maps. Here you can specify the colours you want to see these objects in. For a model you can specify an atom-specific colour scheme.

• Results options : this determines the default sort order for the results page.

• Output options : you can specify if you want the various CCP4 programs to produce logfiles with HTML layout or not. Additionally, you can specify if you want the "SUMMARY" tags to be present in the CCP4 logfiles.

  Note: some programs will not produce proper HTML and might look weird if you use this option! We will have a proper handling of that in later versions - so for now it is not recommended to use this!