Input Files
The FilaSitus/bin directory contains eight data files (in addition to any executables). These files are documented in more detail in the text files themselves, or as follows. You can modify these templates to create arbitrary lattices of actin filaments at any desired level of detail:
  • full_start.pdb: Atomic coordinates of an G-actin monomer as described in Wriggers & Schulten, 1999. Coordinates were placed at the start position of the actin filament structure described by Holmes et al. This file contains no water molecules but all hydrogens and the atomic charges in the PDB occupancy field.
  • nohy_start.pdb: Same structure as above, but no hydrogens so we're looking at ~ half the number of atoms. Since we intend to create many symmetry-related duplicates of the input structure with filabuild, it makes sense to reduce the number of atoms in our model. The charges of the omitted hydrogens have been merged with the charges of the corresponding bonded heavy atoms.
  • pohy_start.pdb: This is a compromise of the two extremes above. Only polar hydrogens (see file-header) have been retained, but the large majority of non-polar hydrogens is omitted. This reduces the file size while maintaining a good quality of the physical properties of the charged and polar groups. This model is frequently used in Molecular Dynamics simulations.
  • resi_start.pdb: This input file contains 376 charged spheres that represent the individual actin residues (see file header for details). Useful if one wants to model filaments on the amino-acid level. The sphere radii are encoded by the PDB B-factor entries. The radii correspond roughly to the radii of spheres that exhibit similar radii of gyration than the encoded residues. Therefore, some of the spheres overlap in 3D space (if elongated residues are represented). The sphere volumes are proportional to the mass of the encoded residues.
  • 4sph_start.pdb: This input files contains only 4 charged spheres, one for each actin subdomain. The sphere radii and positions have been computed based on the Voronoi cells created by Vector Quantization.
  • nohy_start_sd1.pdb: Same as nohy_start.pdb, but actin's subdomain 1 only. This file is used in the tutorial.
  • configure_*.dat: Template files for filabuild. The file configure_36_17_bundle.dat specifies the helical and lattice parameters of an equilateral triangle of actin filaments (in x-y plane). In contrast, the file configure_36_17_sidebyside.dat yields a row of three side-by-side filaments. To switch between the two reprersentations, an angle offset (in increments in 120 degree steps) was applied, otherwise the phases in the center of the triangle would be different from those when the interior is exposed in the side-by-side view. Here each filament consists of 13 subunits in z-direction using 36/17 symmetry. The detailed parameters are explained in the files themselves and in the filabuild documentation. Entries are in free format and the reading stops after all parameters have been read.

The FilaSitus/prepare directory contains some undocumented workflow related to the creation of of the above files (not normally needed by the user).
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