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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