GAMGI Questions: Troubleshooting

# Troubleshooting

- Interfaces
- Formats

### 1. After importing a file with objects, these are not visible.

If the region of space that currently can be seen does not contain the coordinates of the objects in the file, these will not be visible, though everything is fine and working well. Possible solutions are: 1) scale the layer down, so objects become smaller and a larger region of space can be seen at once; 2) if in doubt, use Layer->Select to check which objects indeed belong to the current layer; 3) edit the file and check whether the object coordinates are compatible with the current layer field of visibility. In a default layer, objects have coordinates around (0.0, 0.0, 0.0) and the viewing direction is from positive to negative z axis, so objects with negative z coordinates will be more easily visible; 4) use Layer->Modify to change the layer (projection and position) parameters untill the objects become visible.

### 2. After modifying a layer, the objects become invisible.

GAMGI gives users the flexibility to change all aspects related with visibility and projection of each layer, which can be bad if users do not use this power in a sensible way. Possible solutions are: 1) scale the layer down, so objects become smaller and a larger region of space can be seen at once; 2) if in doubt, use Layer->Select to check which objects indeed belong to the current Layer; 3) use Layer->Modify to change the layer (projection and position) parameters untill the objects become visible; 4) use File->Export to export the current layer to a file, edit the file and remove the layer, and then use File->Import to import the objects to a new, default, layer; 5) Use Undo to recover the previous layer conditions;

### 3. After selecting a visible object, the object is not found.

By construction, each layer is completely independent of the other layers in the same window, even if these are still visible. Therefore, only objects that are in the current layer can be selected directly, otherwise they are not found. This is valid for all objects that a layer can contain, including lights.

### 4. After creating a light, the objects become invisible.

A wired object does not reflect light, so diffuse and specular components cannot iluminate it. When lights are not present, diffuse and specular light components are (0.0, 0.0, 0.0) but ambient light is (1.0, 1.0, 1.0), so objects can be seen. When a light is created, all components are set initially to (0.0, 0.0, 0.0) and wired objects may become invisible, if the ambient light is too small. The solution is to increase the ambient light, using Light->Modify.

### 5. After creating a light, the lights become invisible.

Ambient light is additive, so two lights with ambient components (0.3, 0.3, 0.3) will be equivalent to a light with ambient component (0.6, 0.6, 0.6). When the ambient light is too strong, exceeding the limit (1.0, 1.0, 1.0), diffuse and specular components cannot be seen. Therefore, ambient light becomes (1.0, 1.0, 1.0) and diffuse and specular components become (0.0, 0.0, 0.0), which is exactly the situation when no lights are present. The solution is to decrease the ambient light, using Light->Modify.

### 6. After importing a file with bonded atoms, these are not visible.

In wired mode, unbonded atoms are represented by crosses. When bonds are formed between them, the crosses are replaced by simple lines joining the atoms, changing color at half-distance. If the atoms are in the same position or very close, the line cannot be seen and the atoms and bond become invisible. Clearly this problem only occurs for overlaping atoms, and the solution is to move them to correct positions.
Home