The FilaSitus/bin directory contains
eight data files (in addition to any executables). These files are documented
in more detail in the file headers (or trailers):
-
full_start.pdb: Atomic coordinates
of an G-actin monomer as described in Wriggers
& Schulten, 1999. We use here atomic coordinates based on the McLaughlin
structure of the complex with gelsolin segment 1 due to criticisms of the
earlier Kabsch structure raised by Schutt et al. The differences to the
Kabsch structure are negligible and the 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. New in this file: 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 it is important to add angle offset increments in
120 degree steps, otherwise the phases in the center of the triangle are
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. It is easy to change the length and other parameters of the filaments.
The detailed entries are listed in the filabuild
documentation and in the trailer of the file. Entries are in free format
and the reading stops after all parameters have been read.
In any event, you can modify these
file templates to create arbitrary lattices of actin filaments at any desired
level of detail. |
