ATOMS V6.5 

See the Website www.shapesoftware.com for the latest information on new products and updates.

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HELP AND INSTRUCTIONS

The Help system is accessed through the Help menu, or the buttons in every dialog.

The Instructions in PDF form, included with the distribution, can be printed out.  The contents of the PDF instructions are exactly the same as the Help system.

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IF THERE ARE PROBLEMS

Whenever problems are encountered, the best course is usually to send a copy of the ATOMS data file (.str) which causes the problem(s).  These are ASCII or text files, and may be attached to an email message (send to support@shapesoftware.com).  

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ADDITIONS FOR V6.0
See online Help for further details

1) NEW WINDOWING ARRANGEMENT

In Windows, the "Multiple Document Interface" is no longer used, which means that there is no longer a main or container window.  Child windows, such as text windows and diffraction windows, may exist anywhere on the screen.

In both Windows and Macintosh, a Startup Window appears first, allowing opening, importing or entry of a data set.  When a data set is present, a main Graphics Window appears in place of the Startup Window.  The Graphics window is the parent to other windows such as Text windows and Powder and Precession graphics windows.

2) ROTATION MOVIES

In the Rotation menu. This will write a movie or video file in .AVI (Windows) or .MOV (Macintosh) format. These files consist of a series of bitmap (raster) images. 	

3) POV-RAY FILES

POV-Ray is a program which draws a 3D image pixel-by-pixel, calculating all possible light-ray paths. It allows for much more elaborate lighting effects than the OpenGL software used in the 3D mode in ATOMS. Some obvious effects are shadows and refraction but there are many possibilities. Backgrounds and other objects may be added as well. The files are text (ASCII) and may be edited.
 
The POV-Ray package, with instructions, samples, etc., may be obtained from www.povray.org.

4)  MAGNETIC LATTICE INVERSION

This new option (Shubnikov Tab, Space-Group Symmetry, Input1 menu) reverses or inverts the spin vector for all atoms in the unit cell on alternate translations on the selected axis or axes.  This is equivalent in most cases to a magnetic "wave vector" (or vectors).  It can be used with or without Shubnikov symmetry, and often allows more concise description of magnetic structures. 

5)  DIALOG BAR - FRAGMENTS

This dialog bar allows some basic operations on the positioning and orientiation of individual fragments to be carried out in an interactive way.  Controlled by the Display menu.

6)  RANDOMIZED ATOM CHANGES

The Input1/Atoms-Global option now has a provision for changing the characteristics (such as color or radius) of a given fraction of atoms, on a random basis. This is designed for modelling solid solutions, alloys, etc.

7)  ATOM DELETION TOOL

With the new atom Deletion Tool (Button in the Dialog Bar-Right) you can mark out a polygon on the screen with the mouse, and optionally "delete" all atoms whose centers fall within the polgon in projection.  Actually, the generated atoms are not deleted, they are marked for non-plotting, and they may be restored to visibility at any time.

8)  GENERAL PLANES, LINES AND CYLINDERS

(3D Display Mode only)  This allows drawing planes and lines/cylinders in any orientation.  Planes are polygons specified by points in the crystal (structure) coordinate system - lines or cylinders are also specified by their end points in the crystal system.

Lines/cylinders can be used to show custom "bonds" between any arbitrary atoms.  Such "bonds" can be set up by clicking on the two atoms.

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ADDITIONS FOR V6.1

1)  CORNER AXES

The Input2/Display of Structure Axes option can now show the axes at the corners of the plot.

2)  CHANGES IN ORIENTATION ON RECALCULATE

The current orientation is now preserved when the Calculate option (File menu or Dialog Bar - Left) is excercised instead of returning to the Initial orientation as before.  To return to the Original or Initial orientation use the buttons in the Dialog Bar - Right or the menu option Rotations/Orientation.

3)  Z-MATRIX INPUT

Atomic positions for molecules can now be input in the form of a z-matrix, that is a sequence of bond distances and angles, rather than coordinates on Cartesian or other reference axes.

4)  FULL-SCREEN 3D DISPLAY FOR SHUTTER GLASSES (WINDOWS ONLY)

If you have a CRT display and suitable video card and driver (see especially www.nvidia.com) the image can be viewed in full-color stereo 3D using low-cost shutter glasses.

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ADDITIONS FOR V6.2

1)  HALF-AND-HALF BOND COLORATION

Bonds can now be colored half-and-half in the two atom colors, rather than with a separate color. Input1/Bonds dialog.

2) MOVABLE LABELS

Labels for atoms, bonds and angles can now be individually moved from their centered positions to avoid interference in final (file or printed) output.

3) PROTEIN DISPLAY MODE AND PDB FILE HANDLING

A special protein display mode for data derived from PDB (Protein Data Bank) files shows only the connections of the backbone atoms of the residues (main part of the protein).  Hetatoms are drawn in full (subject to deletion of individual atoms), and individual residues may be selected by number for drawing in full (Protein dialog in the Input2 menu).

Handling of PDB files has been improved, with more information available about residues.

4) IMPROVED CIF FILE IMPORTING

Importation of CIF files has been updated and improved.  The mmCIF (molecular) format is now supported, with reading of PDB data when available.

5)  HYDROGEN ATOM LOCATION

ATOMS can derive the approximate location of hydrogen atoms in data sets, for example proteins, in which they are lacking.

6)  VIBRATIONAL ANIMATION

Files written by VIBRATZ with information on the vibrational modes can imported and shown in animated motion on the screen.  For Windows and Mac, movie/video files (.MOV or .AVI) can be written for display with other software.

7)  SYMMETRY NUMBERS

The symmetry operator number of each generated atom can be shown as an italic superscript, as required in some cases for illustrations in Acta Crystallographica.

8) POV-RAY CAVITIES MODE

V6.0 could already write Cavities-mode files for the ray-tracing program POV-Ray, but in the form of an assemblage of triangles defining the surfaces. This new option will write (smaller) files for POV-Ray which allow that program to use its special Constructive Solid Geometry algorithms to give a higher-quality image.

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ADDITIONS FOR V6.3

This version is primarily a release to update the Macintosh editions for Intel processors and to correct bugs.

1)  THERMAL MOTION ANIMATION (added in V6.3.4)

This requires import of a .MOT file containing the vibrational mode data from the program VIBRATZ (Shape Software).  The overall thermal motions are shown at a series of selectable temperatures.  A movie (video) file can be written by the Windows and Mac versions.

2)  THERMAL ELLIPSOID INFORMATION (added in V6.3.4)

If thermal ellipsoids are displayed, clicking on an atom and then on the Ellipsoid button in the resulting dialog will give the orientation of the ellipsoid principal axes.

3)  GLOBAL CHANGES IN BONDS (added in V6.3.4)

In the Atoms/Bonds-Global option (Input1 menu), the radii, colors and other attributes of all bond specifications can be changed.

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ADDITIONS FOR V6.4

1) Support for Quad-buffered OpenGL 3D stereo viewing. This allows viewing in "true" 3D stereo, using the new generation of special glasses and/or monitors. An nVidia Quadro series graphics card, or other adapter supporting Quad-buffered OpenGL, is required.  Selected in the Drawing Mode (see 4).

2) Support for 3D drawing using Microsoft Direct3D (DirectX) system software.  This allows various types of "true" 3D stereo viewing, using special glasses, monitors or projectors. The 3D Vision stereoscopic system by nVidia, using their GeForce display cards is supported; other systems may also work.

3) Support for Flash (.swf) movie files. This format is usable on all platforms (Windows, Mac and Linux).

4) Changes in display modes. Instead of a single Display Mode giving various combinations of 2D and 3D, ellipsoid and non-ellipsoid, etc. there are now two Modes: 

The Model Mode allows the choice of Standard, which includes ball-and-stick and polyhedrons; Thermal Ellipsoid or Ortep-style drawing; Cavities, showing open space; and Protein, showing the protein backbone and residues in a special way. Standard and Ellipsoid modes can be shown as both 2D and 3D Drawing modes; Cavities and Protein are 3D modes only. Ellipsoids and polyhedra can be mixed in 3D Drawing modes.

The Drawing Mode selects the drawing technique and type of stereo viewing; 2D Single; 2d Stereopairs; 3D (OpenGL) Single; 3D Stereopairs; and 3D Quad Stereo (see 1).

These modes are selected in the Sub-menus of the Display menu, or two drop-downs in the Dialog Bar - Left.

5) Optional Fullscreen display for all types of modes, 2D and 3D, on Windows, Mac and Linux. Selected in the Display menu or a button in the Dialog Bar - Left

6) Skeletal and anaglyph (skeletal) display modes have been discontinued, though there is still an option for skeletal mode during rotation.

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The ATOMS program file, formerly called wxAtoms.exe, is currently named Eragon.exe. This is a temporary expedient which is necessary to allow stereo 3D viewing in a window with the nVidia display cards and glasses.
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ATOMS for Windows V6.4 requires that Microsoft DirectX 9 or later be installed.

If you get a message when you start up ATOMS such as "d3dx9_42.dll not found" you should update to the latest DirectX.  The best way to do this is directly from Microsoft:

http://support.microsoft.com/kb/179113

An alternative, which is not recommended, is to install those files which are needed. As best as can be determined, at least the following are needed:

d3dx9_42.dll
d3d9.dll
d3d8thk.dll

These are usually installed in the \Windows\System32 directory. Installing dll's may require expert knowledge and incorrect installation may damage your system. 

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ADDITIONS FOR V6.5

1) SUPPORT FOR 3D PRINTING. 

Writes .stl and .obj files.  3D Printing option in the File menu.
