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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


Amino acids that delimit the convex hull of the included area. Numbers from 1 to 9999 separated by commas spaces or tabs.


Atoms that delimit the convex hull of the included area. Numbers from 1 to 9999 separated by commas spaces or tabs.


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

Read the input coordinates and write 'include_sphere.ANA' file with the requested pseudo sphere. Deprecated.


Read the input coordinates and write 'include_cylinder.ANA' file with the requested pseudo cylinder. Deprecated.


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


Amino acids that line the desired cavity. Useful for discovering new cavities. Deprecated.


Minimum number of wall atoms of the included amino acids. Deprecated.

  • Default: 2

Clusters options


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

Minimum number of cells a cluster has to have to be included.

  • Default: 2

Accessible Surface Area options


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

Which side to keep. inside: keep inside nulls. outside: keep outside nulls.

  • Default: inside

Residues to exclude from the ASA algorithms.


Minimum dot product to keep(discard) cell. As it increases more cells are classified as being outside.

  • Default: 0.7

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


Frame to begin reading at.

  • Default: 1

Step count to read trajectory frames. NetCDF format only.

  • Default: 1

Frame to stop reading. Reads the whole trajectory when set to 0.

  • Default: 0

NDD options


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

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

If true ANA will scale the input vectors by their frequencies instead of automatically generating its own scaling factors.

  • Default: false

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


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 for grid output.

  • Default: 5

Misc options


Radius of the sphere with the minimum volume to be taken into account.

  • Default: 1.4

Radius of the sphere with the maximum surface to be taken into account. Deprecated.

  • Default: 99

Triangulate only ATOM records.

  • Default: true

atom: output a file with the wall atoms. residue: output a file with the wall amino acids. none: don't.


Separator character for wall residues (atoms). +: might useful for pymol.

  • Default: \t

Instead of triangulating the whole molecule triangulate only the included amino acids. Deprecated.

  • Default: false