Configuration variables
Terminal options
--input_struct, -s
Input structure. This is the only positional argument so you can type it first and skip the flag.
--input_md, -d
Input file with MD simulation.
--config_file, -c
Filename of the configuration file.
--include, -i
Coordinates of the included area in PDB format.
--output_draw, -f
PDB output filename.
--output_vol, -o
Volume output filename.
--output_wall, -w
Cavity's wall atoms/residues output filename.
--NDD_modes, -M
Input vectors for Non-Delaunay dynamics (NDD).
--NDD_frequencies, -F
Input frequencies (in cm^-1) to calculate the flexibility index by NDD.
--NDD_scaling, -S
Input scaling factors for NDD. See ANA's manual to understand why you may want to use them.
--NDD_size, -Z
Scaling magnitude for the input vectors for NDD. Usual appropriate values lie between 4 and 7.
- Default: 1
--NDD_output, -O
Suffix for the NDD output file. The scaling magnitude will be the prefix.
--tool_check_CH, -t
Filename of output PDB displaying the included area. ANA will exit after writing this file and no other calculation will be performed.
--tool_pdb_to_ch, -p
Read the input PDB and write 'include.ANA' file with the vertices of its convex hull.
--tool_pdb_norm, -n
Read the input PDB and renumber its atoms and residues. Be aware that his tool won't fix every error in your PDB. Writes the output PDB to tool_pdb_norm.
--tool_aa_to_ca, -a
Write Calpha atoms indices for the included residues to stdout.
--ver, -v
Output version number.
--help, -h
Output help message.
Configuration file options
Included area options
included_area_residues
Amino acids that delimit the convex hull of the included area. Numbers from 1 to 9999 separated by commas spaces or tabs.
included_area_atoms
Atoms that delimit the convex hull of the included area. Numbers from 1 to 9999 separated by commas spaces or tabs.
included_area_precision
0: keep all cells that intersect in the included area. 1: prune the intersecting cells to keep only the voids that lie inside the included area.
- Default: 0
sphere
Read the input coordinates and write 'include_sphere.ANA' file with the requested pseudo sphere. Deprecated.
cylinder
Read the input coordinates and write 'include_cylinder.ANA' file with the requested pseudo cylinder. Deprecated.
prism
Read the input coordinates and write 'include_prism.ANA' file with the requested prism. Deprecated.
Useful options for outlining the desired cavity with ANA Static
included_residues
Amino acids that line the desired cavity. Useful for discovering new cavities. Deprecated.
minimum_number_of_vertices_to_include
Minimum number of wall atoms of the included amino acids. Deprecated.
- Default: 2
Clusters options
clusters_method
Define the method to clusterize cells. none: don't group null areas. facets: group null areas if the tetrahedrons share facets. boxes: group null areas if the tetrahedrons bounding boxes intersect.
- Default: boxes
clusters_min_size
Minimum number of cells a cluster has to have to be included.
- Default: 2
Accessible Surface Area options
ASA_discard_method
Method for discarding cells according to solvent exposure. none: don't. cm: determine cells surrondings using the global CM as reference. backbone: draw a convex hull between the Calphas and discard every cell with its centroid outside(inside) the hull. axes: determine cells surrondings using its centroid and cartesian axes as references.
- Default: cm
ASA_only_side
Which side to keep. inside: keep inside nulls. outside: keep outside nulls.
- Default: inside
ASA_exclude_residues
Residues to exclude from the ASA algorithms.
ASA_min_dot_pdt
Minimum dot product to keep(discard) cell. As it increases more cells are classified as being outside.
- Default: 0.7
ASA_max_dist
Maximum distance between cell and Calpha used to keep cell. The bigger this number is the better (but slower) the process gets.
- Default: 15
MD options
start
Frame to begin reading at.
- Default: 1
step
Step count to read trajectory frames. NetCDF format only.
- Default: 1
stop
Frame to stop reading. Reads the whole trajectory when set to 0.
- Default: 0
NDD options
NDD_modes_format
Format of the input vectors. amber: vectors will be read as Amber PCA modes. row: vectors will be read in row major order, each row is a vector. column: vectors will be read in column major order, each column is a vector.
- Default: row
NDD_particles_per_residue
Number of particles used to represent each residue. ANA currently support these levels of coarse grain: 0: Full atom. NOT YET SUPPORTED. 1: 1 particle per residue (alpha carbon representation). 6: 6 particles per residue: N;CA;C;O;CB;R (side-chain center of mass). Gly and ALA only have 4 and 5 particles respectively. Be sure to check your PDB is properly formatted and atoms are properly ordered. First the heavy atoms starting with N and then the hydrogens starting with H.
- Default: 1
NDD_frequences_scaling
If true ANA will scale the input vectors by their frequencies instead of automatically generating its own scaling factors.
- Default: false
NDD_step
Number of steps in the NDD pipeline ANA will perform. 1: ANA will not perform the derivative and instead output 2 files with the volumes of the displaced cavity in the positive and the negative direction. 2: ANA will output the VGV. 3: ANA will output the flexibility index.
- Default: 3
Output options
output_type
How to visualize output cavities. raw_pdb: null areas as tetrahedrons. raw_cgo: null areas as tetrahedrons formed with CGO lines in a pymol script. grid_pdb: null areas filled with points. grid_cgo: null areas filled with CGO spheres in a pymol script.
- Default: grid_pdb
sphere_count
Sphere count for grid output.
- Default: 5
Misc options
min_vol_radius
Radius of the sphere with the minimum volume to be taken into account.
- Default: 1.4
max_area_radius
Radius of the sphere with the maximum surface to be taken into account. Deprecated.
- Default: 99
atom_only
Triangulate only ATOM records.
- Default: true
list_wall
atom: output a file with the wall atoms. residue: output a file with the wall amino acids. none: don't.
separator
Separator character for wall residues (atoms). +: might useful for pymol.
- Default: \t
triangulate_only_included_aas
Instead of triangulating the whole molecule triangulate only the included amino acids. Deprecated.
- Default: false