The environment of SHARP/autoSHARP
||© 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.
||(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
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 http://www.ccp4.ac.uk/. 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.
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
- 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.
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
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
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:
- 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
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
- 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
- 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.
are the input instructions to SHARP
(also called SIN files - file extension *.sin) and
autoSHARP (with file extension *.asin)
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
- 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
- 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).
This leads you to the Preferences page, where you can choose some
important parameters of the interface (mainly about graphics and
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
- Job submission
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
Several types of map are available:
- Electron density : ordinary electron density
maps, calculated after heavy atom refinement and phasing
- 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
- 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
- [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
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
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.
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!
Last modification: 31.07.2013