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Atomic Blender - Utilities Panel
The panel helps modifying the properties (radius, etc.) of atoms and sticks, which are part of atomic structures like molecules, clusters, surfaces, etc. The panel can be used in combination with the PDB and XYZ importer and the cluster addon.
UI location Left side, in TOOL_PROPS
Usage Activate the addon in the user preferences (installation see below). After, a panel is visible on the left side in the TOOL_PROPS. More details can be found below.
Version 0.95 (2013-01-24) Author(s) Blendphys (Clemens Barth)
Blender >= 2.64 License GPL
Category Import - Export
Note(s) Please, use Blender version >= 2.64

The panel is useful for the following addons: PDB importer/exporter, XYZ importer/exporter and Cluster


Executable information
File name see files in directory ../scripts/addons/io_mesh_pdb
Current version download io_atomblend_utilities.zip
External Python Modules or dependencies No dependencies
Data A custom data file can be used for the colors and radii of the elements. You can download it from here: custom_file


Warning /
Links Atomic Blender personal pages
Release Log PDB forum

XYZ forum

forum for the cluster addon

Tracker


Quick install

  1. Download the file io_atomblend_utilities.zip from here: Download. (Do not unzip)
  2. Go to Menu: File -> User Preferences ... -> Addons (top)
  3. At the bottom, push Install addon and load the downloaded file.
  4. Search for the Atomic Blender - Utilities script in the addon list and activate it (top right, check box). If the script shall be present after each start of Blender choose Save As Default.
  5. Re-start Blender!

Forum

The addon can be discussed either in the PDB or XYZ addon forum:

PDB forum

XYZ forum

Forum for cluster addon

'Atomic Blender - Utilities' panel

To make life easier during manipulating atoms of imported structures the Atomic Blender - Utilities panel can be installed (Installation: see above). The panel offers some interesting functionalities.

Atomic Blender - Utilities panel

Custom data file

A separate custom data file containing all types of radii and colours of the atoms can be loaded. Such an option is useful when one wishes to use pre-defined values for radii and colours. An example can be downloaded from here: Custom data file.

The custom data file is an ASCII file, which can be duplicated and modified by the user. The radius and/or color of the atoms can be permanently changed as follows: Search the name of the atom and change the radius ('Radius used'). Do the same with the RGB values for the color. The value [1.0, 1.0, 1.0] corresponds to white and [0.0, 0.0, 0.0] is black.

The data file needs to be loaded first. The colours and radii are changed after executing 'Apply'. Note that only selected atoms are changed.

Measure distances

This is to measure the distance of two objects in the Object Mode but also in the Edit Mode. The unit is Angstrom.

All changes concern

This selector determines which objects are subject for changes defined by the options directly below. The changes are either applied on only selected objects or on all objects in the current scene and layer.

Changing the size of the atoms

Change type of radii - With this bool enumerator the type of radii can be chosen. Either one uses pre-defined, atomic or van der Waals radii. The default values for pre-defined radii are the atomic radii. Charge state: For option ionic radii, the charge state can be chosen and the radii of selected objects are instantaneously changed. The best is to first select one type of atom (e.g. only all hydrogens) and then to apply the charge state.

Change atom radii in pm - All radii of a specific type of atom can be manipulated. Type in the name of the atom (e.g. 'Hydrogen') and choose the radius in picometer.

Change atom radii by scaling - This modifies the radii of all atoms with one scaling factor. Type in the scaling factor and increase or decrease the size of the radii by pushing Bigger... button or Smaller... button, respectively.

Changing the size of the sticks

The diameter of the sticks can be changed, too. The buttons Bigger... and Smaller... allow increasing or decreasing the diameter, respectively. The scale factor determines, how strong the change of diamter shall be. By using the outliner (top right), one can apply these operators on only a selection of sticks (e.g., only the sticks of the hydrogens).

Changing the shape of the atoms

It is possible to change the shape (sphere, cube, icosphere, etc.) and material of the atoms. First, select your atoms via the mouse or the outliner. After, you have the following options and functions:

Shape - Choose the shape in the first bool enumerator Shape.

Material - Choose one of the materials in the second bool enumerator Material. The materials are only examples, further refinements can be done in Materials of the Properties panel (left side of the Blender UI).

Special - Here, you can choose an object with a special shape, material, etc. Such objects are quite nice to represent defects in atomic structures. When choosing such a special object, you cannot anymore separately choose the shape and material from above. In Objects and Materials of the Properties panel (left side of the Blender UI) further changes can be done.

Button Replace - After all, push the button Replace. The shape and/or material of all selected atoms are then changed. This option works for objects and dupliverts object structures.

Button Default - If you want to have the default values (NURBS spheres and specific element colors and sizes) of selected atoms push button Default.


Separating atoms from a dupliverts structure

When structures are imported via the PDB or XYZ importer the atoms are put into a so-called dupliverts structure, somewhat into groups of elements (e.g. all hydrogens). Single atoms can be deleted or displaced in the Edit Mode of Blender by modifying the properties (position) of the vertices. However, they are always a part of the structure and are not independent objects. Sometimes one would like to mark single atoms or replace the atoms by something different: Example: Imagine you have a NaCl(001) surface where you would like to replace an atom by an atomic defect in form of a ball with different colour.

To separate single atoms, one needs to select the atoms (vertices) first in the Edit Mode. In the Atomic Blender - Utilities panel, a bool enumerator (Object) and a button (Separate atoms) appear at the bottom. If the bool enumerator remains on Unchanged the type of object (NURBS, mesh, meta) and its properties will not be changed. If desired also an other type of object can chosen, which then replaces the standard type of object.

After having chosen the type of object use bottom Separate atoms to separate the selected atoms: the atoms are then single, new objects, which can be manipulated in any way. They appear in the Outliner and carry the suffix '_sep'.

Converting all atoms of a dupliverts structure to real objects

Do the following: Select the whole structure (molecules, surface, or what ever) with the mouse. Go to objects Apply -> Make Dupliverts Real or just push Shift Control A. With this you produce real objects! In the outliner delete the remaining dupliverts structures, named like 'Carbon', 'Hydrogen', etc.