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). |
