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OVERVIEW
ROTGEN is an X-windows based program for carrying out simulations of
X-ray diffraction rotation images and analysing the unique data
coverage for one or more crystal settings and series of rotations.
A strategy option provides the user with information on the most
efficient way to collect data based on the current cystal setting.
Previously processed data stored in an MTZ reflection data file may be
included in the analyses if required.
The current program incorporates functions from the CCP4 (Collaborative
Computational Project, Number 4, (1994)) and/or the MOSFLM suite
(Wonacott, Dockerill & Brick (1980), Leslie (1992)) programs OSCGEN,
UNIQUE and COMPLETE (the function of the latter now incorporated in MTZDUMP).
The general treatment of the goniometry is derived
from that used in the MADNES program (Messerschmidt & Pflugrath, 1987).
The program makes also use of the XDL_VIEW toolkit (Campbell, 1995), library
routines from the Daresbury Laboratory Laue Software Suite (Helliwell et al.,
1989) and the CCP4 libraries.
The program is in the process of an on-going development. Consideration
is being given to the possibility of integrating the use of the program,
perhaps in a re-packaged form, with the PXGEN interface used on PX stations
9.5 and 7.2 at the Daresbury SRS (Kinder, McSweeney & Duke (1996). It is
intended however that a standalone version will also be retained.
Details of setting up the program can be found in Appendix 1.
In the description of program menus, the menu items available are generally
indicated by the menu button label enclosed in angled brackets.
e.g. <Rotation Simulations> or <Return to Previous Menu>
The user should assume that any prompt/reply sequences take place in
the main text input/output window of the program (see below) unless
otherwise stated. Errors (or warnings) may either be indicated by
messages (to the main text input/output window of the program unless otherwise
stated) or pop-up notices; the description 'message' in the text indicates
the former and the description 'notice' indicates the latter.
List of sections:
Running the Program
Introduction to XDL_VIEW
Screen Layout
Some Basic Concepts
Outline of the Main Options
The Command Window
References
Normally the program may be run by typing the command rotgen though
this will necessarily depend on how the particular system, on which the
program is being run, has been set up. Note also that the environment
variable or logical name SYMOP must point to the CCP4 space group symmetry
operators file (see Appendix 1). By default a log file named
rotgen.log will be created. A few parameters, including the
name of the required log-file may be set to non-default values either
by setting an environment variable (or logical name under VMS) and/or via
a command line argument. Specifications in the command line override
any specifications made via environment variables if both are defined.
The following options are available:
- Setting the log file name
A new log file name may be selected by setting the environment variable
(logical name) ROTGEN_LOG to the name of the required log file. If the value
is 'none' no log file will be written unless specified in the command
line arguments. To specify a log file name via the the command line give
the switch -l followed by the log file name.
- Setting the default orientation for simulations
A new default value for the simulations orientation may be set via the
environment variable (logical name) ROTGEN_ORIENT. Valid values are
'ipdisp', 'denzo' or 'oscgen' (case insensitive). To set the default
orientation via the command line, give the switch -o followed
by one of the code strings given above. If no valid option is set via the
comand line arguments or the environment variable, the program
default is the 'ipdisp' orientation. (Note: the apostrophes are not part
of the code strings)
- Setting a different font
A different size of font to be used for the parameter tables, menu area,
io-window etc. may be chosen by setting the environment variable
ROTGEN_FONT to a value from 1 to 5. The default value is 2. (See also the
XDL_VIEW documentation on how to reset the 5 fonts and font sizes used
by that package). The font size cannot be selected via a command line
argument.
- Changing the parameter updates policy
The parameter updates policy (described below) may be changed by setting
the ROTGEN_UPDATE environment variable or via the -u command line
flag. Valid values for the environment variable or keyword following the
flag are 'yes' (the default), 'no' or 'warn'.
Example of setting options via command line arguments:
rotgen -l lys_rot.log -o denzo
Other command line arguments for setting the program mode (not currently
relevant) are described in Appendix 1.
XDL_VIEW is a set of X-windows based routines providing 'view-objects' for
various functions such as menus, parameter tables, image displays and
text input/output.
View-objects, which can return data to the calling
program, will normally contain an 'active strip'. This indicates
whether or not the program is currently awaiting input from that object.
It consists of a square
at the left hand side and a rectangle at the right hand side, usually
stretching across the width of the view-object. When
the program is ready to receive input from the menu, then the
square is filled with green (or black on a black and white display)
and a message is displayed in the rectangle. When the
program is not waiting to receive input then both parts of the
active strip are cleared. A program may be waiting to receive input
from more than one view-object at a time and from different view-objects
at different times and hence the reason for indicating to the user
the current 'active/inactive' state of any particular view-object.
The view-objects are basically designed for use on a colour display
but will work, with limitations in some cases, on a monochrome display.
For ROTGEN, a colour display should be used if at all possible and
the documentation assumes the use of such a display.
Default fonts will normally be used but some user selection is possible
(See Appendix 1).
Reference should be made to Volume 1 of the XDL_VIEW documentation to find
detailed instructions on how to manipulate the various view-objects
used by the program.
- Note:
- When running an XDL_VIEW based program such as ROTGEN, do not attempt
to dismiss any of the windows displayed using the window manager options
as this will cause the whole program to exit. ROTGEN is designed so that
all windows will be automatically deleted by the program when appropriate.
The basic screen layout for the program is divided into five areas.
Figure 1 Main Screen of ROTGEN
- Top Left
- A menu area used for selecting the options currently available.
The options within a menu are, in general arranged such that
the normal order of access would be from the top downwards
without necessarily using all the options available. The
basic menu structure of the program is hierarchical and most
menus have an item at the bottom which returns the program to
the previous level with a label such as <Return to Main Menu>
or <Return to Previous Menu>
- Top Right
- Main parameter table. This is an editable parameter table which
contains the main crystal/detector parameters.
- Bottom Left
- Parameter table 2. This area is used for special purpose
parameters relating to the current option selected.
- Middle right
- This area is the main text input/output window. This is
used to output textual information from the program when
required and also, at some stages, for prompt and
reply sequences e.g. for inputting file names.
- Bottom Right
- Command window. This window is for inputting program
options and parameters via a command line. Keyworded parameter
values may be input or inspected. It is anticipated that
processing functions will be added at a later stage.
Additional windows e.g. windows for displaying Rotation simulations or
graphs are used at various stages of the program. These
may be positioned independently of the main program window. Normally
they will initially be positioned just to the right of the menu area.
- The Parameters
The parameters used by the program form a keyworded data set. They fall
essentially into two categories:
- The crystal parameters such as the crystal system, lattice type,
cell parameters, crystal orientation parameters and the resolution
limit of the diffraction.
- The parameters relating to the X-ray and detector system and
X-ray source such the wavelength and the positioning of the detector.
The parameters include specifications for one or more crystal orientations
and sets of images. Some parameters refer to the dataset as a whole and
some may have separate values for each of the crystal sets.
The parameters used in ROTGEN are described in Appendix 2.
- Current Set
The program is designed to allow for processing data from several
crystal sets. A crystal 'set' means a particular crystal orientation
and a rotation range. The basic crystal form (e.g. space group) is assumed
to be the same for each crystal set within the dataset. The current
crystal set (and current image where relevant) may be selected via the
main parameter table.
- Resolution
One of the main functions of the program is to analyse data coverage
in terms of the unique section of the reciprocal lattice for the space
group in question. The resolution used to determine the unique data
is that specified for the first crystal set and this fact should be
borne in mind if a different resolution limit is set for the different
crystal sets. When analysing MTZ data alone, the resolution value from the
MTZ data file may optionally be used instead.
- Parameter Updates
By default, most parammeter values, reset via the main parameter table for
the first crystal set, are automatically applied to any subsequent sets.
Exceptions to this are the parameters which define the rotation ranges,
ROTSTART, ROTEND, ROTS2, ROTE2, ... ROTS5, and ROTE5. This updating may
be disabled or changed to give a warning via a pop-up notice, allowing the
user the choice of whether or not to update, by setting the ROTGEN_UPDATE
environment variable or via the -u command line flag. When parameters are
updated via the command window, the normal keyword conventions apply
i.e. that the parameter will apply to all sets if it has no attached set
specification or to a single set if a set is specifiied (see Appendix 2 for
more details of the parameter keywords).
- Program Modes
The program is basically designed with the possibility of being run in
three different modes though only the (default) interactive mode using
X-windows has been developed to date. The other two modes are a terminal
mode and a batch mode. It is anticipated that commands will be written
to carry out some of the processing functions now done interactively.
These could also be requested via the programs's command window when
running in interactive mode.
The following are the main options available in ROTGEN selectable via
options in the program's main window and menu:
- Setting up the parameters
The parameters in the main parameter table are assigned
default values when the program is started. Individual
parameters may be reset by editing the values directly
in the parameter table (see XDL_VIEW documentation). A new
set of parameters may be read in from a keyworded parameters file
using the 'Read Parameters File' option.
Activating the 'edit' menu item associated with the 'detector--->' item
brings up a new window to allow the values of detector parameters, not
displayed in the main parameter table, to be edited. This new window will
be automatically removed if no input is received over a period of a minute.
When the required parameters have been set up, they may be
saved in a keyworded parameters file for future use using the 'Write
Parameters File' option.
- Updating the orientation parameters.
The 'Read Matrix File' option may be used to reset the parameters which
define the crystal orientation using matrices produced following auto-indexing
by programs such as REFIX or DENZO. The orientation parameters may also
be written out for subsequent use with the MOSFLM or HKL (DENZO) packages.
- Rotation simulations
Two basic types of simulations are available, 'colour' simulations
and 'interactive' simulations. In each case a window is created with
a display area for the simulation, an area to list details of a selected
reflection, a control panel and an area used for requesting hard
copy (Postscript) output of the simulation. 'Colour' simulations
show the show the rotation patterns with the spots colour coded in a
number of different ways. 'Interactive' simulations are in black and
white and have a slider which allow the user to investigate the effects
of changing various parameters such as the oscillation range and
mosaicity; spot labelling is also available.
- Input MTZ data
This option enables the input of previously processed data to be included
in the data coverage analyses provided by the program. The reflection data
must be stored in a MTZ format reflection data file (unmerged or merged).
Some care needs to be taken when interpreting analyses including such
MTZ data as not all the information normally used in the analyses is present
in the MTZ files.
- Analyse data
This option enables the prediction of the reflections which
would be recorded for the defined crystal sets and to analyse the
data coverage in terms of the unique data for the space group, cell and
resolution. The analysis may be done for either the current crystal set
or for all crystal sets within the data set. The results may be presented
in the form or histograms describing the data coverage or in terms of
a pictorial representation of the reciprocal lattice sections. The
analysis data equivalent to that displayed in the histograms is also written
to the log file. The analyses automatically written to the log file exclude
any spatially overlapped reflections. There are options for 'quick' analyses
which examine the data coverage within the rotation range as a whole; these
may be further speeded up by dividing the cell size (internally within the
program) when carrying out the calculations. A further option enables
an alternative and quicker analysis of spatial overlaps.
- Strategy
This option assists the user with determining the best rotation ranges to
be used to maximise the data coverage following an orientation determination
(made using for example REFIX or DENZO) for a crystal. Results are presented
for both a single contiguous rotation range and, optionally, for two
non-contiguous segments. There is also an option to determine a series
of up to five successive rotation ranges each optimised for data collection
following the collection of the previous segments. The data coverage
maximised may either be for the unique data or for acentric pairs data.
Options are available to analse spatial overlaps so that a suitable
oscillation angle may be selected for the data collection.
The command window is intended for use with non-interactive commands for
processing the data which have not yet been developed. However it has
a few useful functions available. These are:
- Type in the command defaults to reset the program default values
for the parameters and internal program flags.
- Input of parameter Keyword/value pairs. This provides a means of
inputting values of parameters which are not displayed in the
parameter tables as well as those which are.
- Showing the value of parameters including those not displayed
in ROTGEN's own parameter tables. These are obtained by typing
a question mark followed by the keyword for the parameter e.g.
?oscrange
For crystal set specific parameters which are given without an
explicit set specification, the value for the current set is shown.
Campbell, J.W. "XDL_VIEW, an X-windows-based toolkit for
crystallographic and other applications" J. Appl. Cryst. (1995), 28, 236-242
Collaborative Computational Project, Number 4 "The CCP4 Suite: Programs for
Protein Crystallography" Acta Cryst. (1994) D50, 760-763
Helliwell J.R., Habash J., Cruickshank D.W.J., Harding M.M., Greenhough T.J.,
Campbell J.W., Clifton I.J., Elder M., Machin P.A., Papiz M.Z. and Zurek S.
"The Recording and Analysis of Synchrotron X-radiation Laue Diffraction
Photographs" J. Appl. Cryst. (1989) 22, 483-497
Kinder S.H., McSweeney S.M. and Duke E.M.H. "PXGEN: A general purpose
graphical user interface for protein crystallography experimental
control and data acquisition" J. Synchrotron. Rad. (1996), 3
accepted for publication.
Leslie A.G.W. In CCP4 and ESF-EACBM Newsletter on Protein Crystallography
(1992) No. 26, DRAL Daresbury Laboratory, Warrington, WA4 4AD, England
Messerschmidt A. and Pflugrath J.W. "Crystal orientation and X-ray pattern
prediction routines for area detector diffractometer systems in macromolecular
crystallography" J. Appl. Cryst. (1987) 20, 306-315
Wonacott A.J., Dockerill S. and Brick P. "MOSFLM program" (1980) Unpublished
Notes.
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