ASSA
Brief Instructions for the
Users ( SGI Version )
Electronic
reprints Copyright © International Union of Crystallography
E-mail: Svergun@EMBL-Hamburg.DE
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Introduction |
WHAT IS ASSA?
ASSA is a 3D graphics interface for interactive display and analysis of macromolecular structures using small-angle scattering. Two major applications of ASSA are:
(1) 3D molecular model rendering
and
(2) graphics interface to the algorithms for solution scattering data
processing.
In fact, ASSA is a complex of programs combined in a single module with a 3D graphics interface.
GETTING STARTED
The following program executables compiled under IRIX 6.4 should be placed in a directory included into the PATH variable:
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1plot |
2D plotting |
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alm22int |
intensity from two bodies |
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assa |
main program |
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intflm |
intensity from Flm coefficients |
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trans6 |
surface from Flm coefficients |
The directory $HOME/Assa (which must be also included in the path) should contain the following auxiliary files:
fib14bin.ph
fib07bin.ph
atom.sld
assa.rgb
The program is started with the command
assa [-p]
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-p: |
with this modificator ASSA selects the best single-buffer type of graphics representation available at the user's workstation. The rendering quality is enhanced at the expence of some technical features. Use it to prepare a high-quality picture for the final presentation of models and their configurations. |
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3D Graphics |
FILE FORMAT
ASSA works with two types of models:
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(a) |
Atomic structures in a standard PDB file format (PDB-objects) |
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(b) |
Low-resolution envelope models resulting from solution scattering data processing: binary files with the extension "sld" (SLD-objects) created by the programs "sasha", "crysol" and "flm2sld". |
LOADING A NEW STRUCTURE
To load a new object into ASSA use the File-Load option from the main menu in the upper right corner. By default, the objects are loaded "as is". The geometrical center of the object can be moved to the origin or to the coordinates specified by the user. The object can also be rotated by specifying the Euler angles. The file name is either selected by browser (<Browse> button), or specified by typing the file name in the text field of the command dialog. After the <Load> button is activated, the object is loaded into ASSA from the specified file. By default SLD-objects are rendered as smooth envelopes and PDB-objects as markers with lines connecting backbone atoms.
ACTIVE OBJECT
All operations are always applied to the
currently active object. Any loaded object can be selected as active either
with the
TYPES OF GRAPHICS
REPRESENTATION
The graphical rendering toolkit is located just
under the main menu. Only the active object is affected. SLD-objects can be
represented as wireframe models, facet surface or Gouraud-shaded smooth
envelope.
The transparency coefficient has an effect only if the transparency option is
ON (<Option-General-Transparency>). For the PDB-objects there is a
non-exclusive choice of rendering of the backbone chain with an adjustable
width, or the entire set of atoms (markers or 3D balls of adjustable size). The
characters indicating the backbone chain atoms in PDB-file can be specified in
the main menu (<Option-General-Chain atoms>, default is "CA").
Residue numbers can also be shown (<Numbers: On>).
TRANSFORMATION TOOLS
Shifts and rotations of the active object are
implemented either with the transformation sliders, by the mouse and by the
keyboard hotkeys. The sliders are moved with the left mouse button. To shift
the active object, click the selected object on the screen, then press and hold
the right mouse button while moving the mouse. These transformations are
implemented either in smooth (default) or in discrete modes (
Table of transformation hotkeys
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Arrow Up |
-- |
Rotate around X axis (clockwise) |
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Arrow Down |
-- |
Rotate around X axis (counterclockwise) |
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Arrow Left |
-- |
Rotate around Y axis (clockwise) |
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Arrow Right |
-- |
Rotate around Y axis (counterclockwise) |
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Insert |
-- |
Rotate around Z axis (clockwise) |
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Delete |
-- |
Rotate around Z axis (counterclockwise) |
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Shift + Arrow Up |
-- |
Move up along Y |
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Shift + Arrow Down |
-- |
Move down along Y |
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Shift + Arrow Left |
-- |
Move left |
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Shift + Arrow Right |
-- |
Move right |
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Shift + Insert |
-- |
Move up along Z |
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Shift + Delete |
-- |
Move down along Y |
To specify the anglular and spatial steps for keyboard
movements use
<Options-General_Keyboard rotation angle> (default is 11 degrees),
<Options-General_Keyboard shift vector> (default is 5 Angstroem).
The information about the current position of the
active object is displayed in the information window
(<Options-Information>).
To return the active object to its initial position use the button
<Reset>.
The transformation center can be fixed to the specified residue with the
<Center> toolkit (only for PDB-objects).
COMPARAISON OF MODELS
To compare PBD- and SLD-models of the same particle, be sure to load the corresponding PDB-object to the center of coordinates (<File- Load-ResetTo_0>). The SLD-object will be centered automatically, unless an other position is specified (see "LOADING A NEW STRUCTURE"). Use transparency (<Options-General-Transparency>), and ROOT transformation to get the best view.
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Program Interface |
MODEL SCATTERING CURVE
EVALUATION
For the active object of any type (except for ROOT and the group of objects) the model scattering curve is evaluated by activating the <Command-Intensity curve> option. The curve is plotted in a separate window.
INTERACTIVE RIGID BODY
REFINEMENT
Mutual orientation of two subunits in a complex particle can be modelled interactively, provided the scattering amplitudes of the subunits are precalculated and saved in the current directory in files with the same names as the structure files with the extension "alm". This is performed by FLM2ALM for SLD-objects and by CRYSOL for PDB-objects.
The procedure is started from a pop-up command window(<Command- Complex intensity>). The meaning of the first 4 parameters:
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1. Input data file |
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Input file containing experimental data to be fitted |
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2. Output file |
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Output file containing the currently plotted fit |
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3. Angular units |
--- |
Units of the abscissa in the input file: |
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Value |
Meaning |
Units |
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1 |
4*pi*sin(theta)/lambda |
1/angstrom |
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2 |
4*pi*sin(theta)/lambda |
1/nm |
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3 |
2*sin(theta)/lambda |
1/angstrom |
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4 |
2*sin(theta)/lambda |
1/nm |
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4. Fitting range |
--- |
Which part of experimental data to fit |
After specifying these parameters the subunit objects can be selected either by typing their names in the text fields, or by mouse click in the graphics area. ASSA warns the user if the input is incorrect or incomplete.
The <Start> button runs the program "ALM22INT", calculating the fit of the scattering intensity of the complex to the experimental data. The fit is plotted on a separate window and remains on the display at the user's disposal.
To check the effect of changes in the subunit positions to the goodness of fit the button <Start> should be simply re-activated. The new plot will appear on another separate window on the top of the previous ones. The maximum number of simultaneously available plots is 20. If this number is exceeded, ASSA will suggest to close some of the plot windows before re-activating the fit program. The current fit is saved onto the output file specified by the user.
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HINT: |
In the vicinity of the optimum position it is reasonable to use keyboard hotkeys to transform the subunits and to set small values to the spatial and angular steps (see "TRANSFORMATION TOOLS"). |
The button <Reset> should be activated if the composition of the complex or some of the input parameters are changed.
EXAMPLE OF INTERACTIVE
MODELLING WITH ASSA
Suppose you have measured the scattering curve (ab.dat) from a complex of two domains, A and B, and their atomic models are available (say, a.pdb and b.pdb). To fit the experimental scattering curve, the following should be done:
1. Compute the scattering amplitudes from the two structures using "CRYSOL" (up to L=10). If the scattering from them was not measured separately, use default contrast in the shell and default volume of the atomic group.
NB: the number of points, maximum order of harmonics and the maximum scattering vector value MUST be EXACTLY the same for the both structures. The maximum scattering vector should be larger than that in the experimental curve ab.dat.
2. Rename the amplitude files you obtain (e.g., a00.alm and b00.alm to a.alm and b.alm, respectively).
3. Start ASSA and load the two structures a.pdb and b.pdb (see "LOADING A NEW STRUCTURE").
4. Start the modelling process with the <Command_Complex Intensity> tool (see "INTERACTIVE RIGID BODY REFINEMENT"). If the domains have been measured at different contrasts, this can be taken into account by the pre-multipliers specified in the command window.
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HINT: |
if the modelling in ASSA does not work, try to start "ALM22INT" separately to find out what the problem is (it is an interactive program as well). Usually one of the needed files does not exist in the current directory, or "*.alm" files do not fit to each other. |
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Saving the Results |
SCREEN ARCHIVING
The configuration of the object on the screen can be saved onto archive files (<File-Save>), and subsequently restored from them (<File-Restore>). The archive format is described in the first 3 lines of the archive files. It includes the number of objects, file names, absolute positions, graphic features (color, style of representation, transparency coefficient etc) and the corresponding annotations. The archive files can be edited manually to obtain desired configuration of the restored objects.
PDB FILE SAVING
There is a possibility to save a PDB-object in its actual position directly into a specified PDB-file (File - Save PDB). This is convenient for saving the results of interactive rigid body refinement (see "INTERACTIVE RIGID BODY REFINEMENT")
PICTURE SAVING
SGI/DEC version of ASSA has a built-in screen-saver in Postscript format (File->Save pst; the program MUST be started as “assa –p!!) One can also use any of screen grabbers available for SGI (e.g. that in mediarecorder), and then use "imgview" to edit and/or print the image.
1.12.1999, Hamburg.