Chimera_BILD

Implementation of some BILD format commands as a Chimera extension, to work directly with them in the Chimera's command line.

Installation (Linux):

1 - If you don't have Chimera installed, download the latest stable copy and install it with:

chmod +x chimera-*.bin && ./chimera-*.bin

2 - If you don't have git installed, install it with:

sudo apt-get install git

3 - Install the chimera_BILD extension with pip (substituting <$PATH> by the path where you want the extension to be installed):

pip install -U git+https://github.com/josan82/Chimera_BILD.git -t <$PATH>

4 - Register the chimera_BILD extension in UCSF Chimera: You have to add the <$PATH> where you installed the extension in Favorites -> Preferences -> Category:Tools dialog of UCSF Chimera.

Usage of the commands:

• In all commands, the color parameter can be set as a name or as a RGB code: The name can be a built-in name, a name defined previously with colordef, or an integer that refers to the old BILD color wheel (0-65, inclusive). Alternatively, a color can be described by its red (r), green (g), and blue (b) components, each in the range 0-1, inclusive. Any transparency in the color is ignored, but transparency can be set separately.

• In all commands, the transparency parameter (optional, default 0) can be set with a value of a range from 0.0 (not transparent) to 1.0 (completely transparent).

• In all commands, the id of the Chimera's object that will be created can be set with an integer value with the optional paremeter id (default 100).

For now, the following commands are implemented to use in the command line of UCSF Chimera:

arrow x1 y1 z1 x2 y2 z2 color [transparency] [r1] [r2] [rho] [id]

Draw an arrow from (x1, y1, z1) to (x2, y2, z2). An arrow consists of a cylinder stretching from the initial point to an intermediary junction, and a cone stretching from the junction to the final point. The radius of the cylinder is r1 (default 0.1), the radius of the base of the cone is r2 (default 4*r1), and the fraction of the total distance taken up by the cylinder is rho (default 0.75).

box x1 y1 z1 x2 y2 z2 color [transparency]

Draw a box with opposite corners at (x1, y1, z1) and (x2, y2, z2).

cone x1 y1 z1 x2 y2 z2 r color [transparency] [open] [id]

Draw a cone with a base of radius r centered at (x1, y1, z1) and a tip at (x2, y2, z2). If the optional parameter open is True (default is False), the base of the cone will be invisible.

cylinder x1 y1 z1 x2 y2 z2 r color [transparency] [open] [id]

Draw a cylinder with radius r and bases centered at (x1, y1, z1) and (x2, y2, z2). If the optional parameter open is True (default is False), the bases of the cylinder will be invisible.

sphere x y z r color [transparency] [id]

Draw a sphere centered at (x, y, z) with radius r.

vector x1 y1 z1 x2 y2 z2 color [transparency] [id]

Draw a line segment from (x1, y1, z1) to (x2, y2, z2).