General program features:

	Batch processing of patch-clamp recordings   (|||image) Input and output in the Axon ATF format (|||image). Piecewise file processing - handles ~unlimitedly large files (~4 Gb). Files can be zipped to reduce file disk size.  Batch processing of the list of files. Scaling of the current or pressure amplitudes Fusion of current and pressure recording channels into one trace Connection of several traces into one long trace Reconstruction of the pressure channel using external approximated data Removing a piece from the middle of the trace Automated correction of the baseline
	Batch creation of 2D all-point histograms   (|||image) Probability over current-pressure or current-time dimensions  (|||image) Arbitrary ranges of histograms. Arbitrary predefined number, width or explicit boundaries of bins. Output saved as a readable plain text file Both discrete steps and continuous ramps of pressure can be treated equally well.
	Conditional 2D histograms creation   (|||image) Traces may be automatically processed so that only selected fragments or points will be counted. E.g. only channel transitions, pikes or substates will be included  (|||image) Flexible set of conditions (23 condition types x 8 range types) allows to describe practically any pattern of channel activity or specific points of interest. Combination of 3 conditions can be used  (|||image).  The selected points are marked in a control output ATF file, so all the included fragments can be visually inspected in Clampfit.
	Batch processing of the created 2D histograms (|||image) 2D histograms crated in the previous steps can be reloaded for additional processing Rebinning of the histograms into smaller or larger number of bins, automatically calculated, defined by bin width, or explicitly specified. Histograms can be automatically rebinned according to pressure steps. by mi When number of points increases after rebinning or in case of the missing data points 2D histograms can be interpolated with 1 of 6 functions  (|||image) Histograms can be rebinned automatically according to steps in pressure in order to maximize data reliability Data can be properly normalized thus compensating for nonuniform pressure steps or ramps Histograms can be neighbor-averaged in either direction to reduce the noise and compensate for bins undersampling (if necessary) Any range of histogram can be zeroed. Any bins can be removed or added. Current and pressure axis can be normalized, e.g. to produce relative current from 0 to 1, or pressure normalization relative some benchmark (like MscL relative to MscS channel)
	Batch creation and processing of 1D histograms (|||image) on the basis of 2D histograms  (|||image, image) Selected range of 2D histogram can be traced into one or several 1D histograms. Tracing along the current axis produces conventional all-point occupancy histogram (|||image), whereas tracing along the pressure axis (with proper conversion and weighting (|||image)) leads directly to dose-response and activation curves (|||image). Values in 1D histograms can be interpolated and tracked with the cursor, so that numeric values can be extracted (|||image) Explicit histogram bins boundaries can be shown (|||image) 1D histograms can be saved in plain tab-separated text files importable into Excel
	Automated or manual fitting of 1D histograms with a set of normal distributions for substates decomposition (|||image, image) 1D histogram from the file or from memory can be fitted with arbitrary number of normal distributions  (|||image) Position, width and height (i.e. amplitude or substate occupancy) of normal distributions are independent tuning parameters Fully automated (global optimization of all the parameters for all the selected distributions), semi-automated (automated optimization of one parameter of one distribution), or manual modes are available Dual control of the fitting quality - visual  (|||image) and by the numeric estimation (|||image) of fit-target deviation. Several weighting functions for deviation estimation are available All the results and tuned parameters are saved in text files and snapshots, and can be loaded as a preset for the next histogram fitting
	Batch plotting of 2D and 1D histograms (|||image, image) Either individual or set of 2D or 1D histograms can be plotted directly from the program. Zoom, cursor (|||image) and 3D rotation features of Matlab are available. For 2D histogram a wide range of representations and coloring is available (|||image, image, image, image)

General program features:

	Batch processing of files (|||image) Expandable two-window interface (|||image). PDB mainboard window is permanent and allows consistent file browsing and processing mode selection (|||image). Options window is different for every selected mode. List of PDB, volumetric data or other files can be processed at once as a batch For regularly numbered files (e.g. file000031.pdb ... file125672.pdb) the list can be generated automatically (|||image). Length of file list is unlimited, that allows to overcome Windows limitation of using file dialog for browsing more than ~1000 files at a time (you can have much more as PDBs of simulation time frames). File list can be loaded from the text file (for complex and long file selections) All data input files (PDB, volumetric, VRML, txt) and most of output files can be in ZIP format, allowing to reduce file size dramatically (5 to 200 times)
	Property profiles creation (|||image, image) For PDB structures containing some values in beta or charge (or other) column (|||image, MscL colored by the atom hydration energy contained in the beta column), the molecule can be divided into slices normal to some axis and sum of the values within every slice can be calculated. In this manner profile of hydration energy or net charge along the channel axis can be calculated (|||image) (profile can be smoothed using PDBAN, see below) Optionally only atoms marked by some value in another column can be considered, e.g. only atoms facing the pore interior, as marked by -1 value in the occupancy column, will be added to the pore hydration energy profile (|||image) Both linear (along the axis) and circular (around the axis) profiles can be computed, so that distribution of hydrophobicity around the channel can be estimated.
	Property profiles averaging (|||image) Original property profiles are usually rough with 1-Angstrom resolution (|||image). They can be smoothed to imitate atoms thermal motion and reveal general features (|||image) Running average, triangular-shaped average, normal distribution or arbitrary neighbor coefficients algorithms can be used for profile averaging. Arbitrary degree of averaging can be used Averaging for circular profiles is available
	PDB column replacement (|||image) External data (from the text file or GetArea output file) can be introduced into PDB file. It can be used to combine calculated hydration energy per atom GetArea with the atomic coordinates contained in PDB Arbitrary column can be copied from one PDB file to another. Batch processing for file lists is available Data per individual atom or per whole residue can be used and spread over all residue atoms. Data per one monomer can be spread per whole homooligomer. E.g. In this way evolutionary conservancy data per residue per monomer can be properly spread per every atom (for future visualization and calculations)
	PDB residues renumbering (|||image) Sometimes during model building in external programs the same block of atoms (e.g. water cube) is duplicated several times over the system, thus leading to duplicate residue numbers for the same segment name. It presents a problem for PSFGEN program. It can be solved by using this renumbering mode of PDBAN Batch renumbering is available
	Property profiles combining (|||image) Different property profiles can be computed with the previous options of HISTAN (e.g. hydration energy profile and slice surface area profile). They can be combined in certain manner to estimate some derived property profile (e.g. energy divided by area to estimate HE density profile)  Profiles can be added, subtracted, multiplied, divided, rebinned (to produce the same number and location of bins in two profiles) or rebinned with spline interpolation Batch combining is available
	PDB structure reorientation (|||image) PDB structure can be automatically reoriented by the combination of criteria. E.g. bundle of alpha-helices can be aligned along the z axis using the rings of selected alpha carbons as a criterion Directed random search algorithm compatible with arbitrary atoms combinations is used
	PDB property 3D averaging (|||image) Some properties, like atomic hydration energies, are distributed quite non-homogeneously on the protein surface. This makes it difficult to grasp visually. With this option the properties of individual atoms can be averaged among them and reintroduced into arbitrary columns of PDB file, so in can be used in external visualization programs Optional inclusion of only desired atoms (marked by certain values in the indicated column), so hydration energy or charge can be averaged only among pore-facing atoms)  (|||image) Optional usage of some column as a multiplying coefficient, so that property can be distributed proportional to the exposed area of the atom Additive, averaging and weighted averaging methods are available
	Volumetric data creation (|||image, image) PDB coordinates can be used to create 3D volumetric density arrays. These volumetric data can be used later in other PDBAN modes for pore crossectional area calculations (|||image, image), surface (|||image), or density (|||image) visualizations. Volumetric data can be created as an average of multiple input files, reproducing time-averaged density Volumetric data can be smoothed in space reproducing thermal motion of atoms (using normal distribution or multistep nearest neighbor averaging). It can be used to enhance principal structure geometry in visualization purposes (|||image) and for virtual 'reconstruction' of low-resolution AFM images  (|||image) Arbitrary sets of VDW radii can be supplied for volumetric data creation VDW surface, surface created by the spherical probe center or probe surface can be used. Probe radius can be arbitrary Automatic or predefined size and step of volumetric greed Batch processing and ZIPped input/output of the files Optional output in the Matlab binary or plain text formats
	Crossection area calculation by volumetric/PDB/VRML data (|||image, image, image) Volumetric (preferable), PDB, and externally created VRML surfaces (|||image) can be used to compute channel crossectional areas profiles Choice of 5 methods of crossectional area calculations (some are specific to certain input file formats) The surface is created (|||image), then divided into slices (|||image) and crossection areas (|||image), effective radii (|||image), and perimeter lengths are computed (|||image) Three methods of crossection areas sorting are available - it facilitates postprocessing of the output in the external spreadsheet programs Arbitrary orientation and step of crossection planes set Batch processing is available Option to plot results on screen, automatically save text files and images, or send them to printer Optional output of the triangulated channel surface in plain text format (e.g. for the import of calculated averaged surface into VMD)
	Channel conductance calculation by radius profile (|||image, image) Provided the channel pore crossectional area profile or crossectional radius profile was computed, and conductivity of the medium is indicated, the pore resistance profile can be computed in Hille's approximation (|||image). The method works fine for the large nonselective pores (like MscL, MscS or hemolysin) Ion radius size and hydration shell thickness can be taken into account and subtracted from the effective pore radii Pore access resistances are taken into account, and the total channel resistance is estimated Output results can be saved as a plain text files Batch processing is available Option to plot results on screen, automatically save text files and images, or send them to printer
	Volumetric data visualization (|||image, image) Volumetric data calculated in PDBAN can be visualized with a broad set of representations (|||image) Surfaces can be created at the given levels of density. Can be used for channel surface visualizations (|||image) and for representations of 3D distributions of water density in the channel (|||image, image). 2D density maps can be computed as an average or sum between 2 parallel planes. Similar maps can be created for the angular sector created by two intersecting planes. Map (|||image) or landscape (|||image) representations are available 3D data can be averaged with arbitrary degree of rotational symmetry (|||image, image) Linear profile can be created as a crossection of 2D map (|||image), both linear and circular variants are available, as well as contours at the desired probability level. Optional averaging over 2D region.
	Volumetric data combining (|||image) Different 3D volumetric datasets can be computed with the previous options of HISTAN (e.g. total number of hydrogen bonds in some volume and water density there). They can be combined in certain manner to estimate some derived property profile (e.g. number of hydrogen bonds in space divided by the water density will produce the degree of water H-bonding when it occupies the selected area (excluding time moments of dewetting)  (|||image))  Profiles can be averaged, added, or divided Profiles can be scaled by arbitrary weight coefficients (e.g. to compensate for the different simulation times over which hydrogen bonds were counted) Batch combining is available

General program features:

	Reads gel images in the BMP or TIFF formats (|||image). Images should be prepared to indicate columns (see included ReadMe.txt file) (|||image).
	Output consists of text files containing band width, total amount of darkness, and protein concentration
	When imported into any spreadsheet program they produce digitized profile of gel darkness (|||image)
	After proper baseline correction (|||image) protein content profiles (|||image) and histograms (|||image) can be computed.

Expanded GETAREA library of atom types - it is compatible with wider range of PDB structures, including PDBs created by PSFGEN with CHARMM22 topology settings.

Atomic solvation parameters by Wesson and Eisenberg 

	in kcal/mol/angstrom2
	in dacal/mol/angstrom2  - for higher precision per-atom output

Script for MS WORD (written in MS Visual Basic) for correction long (4-letter) atom names in PDBs produced by PSFGEN or VMD to make them readable by GETAREA. The script can be inserted into MS Word template (e.g. through Tools->Macro->Macros->Edit)

coordinates2dcd - Script reading coordinate files (in any VMD-readable format - NAMDBIN, PDB, DCD, etc.), adding them all as frames in trajectory and saving the trajectory in peaces (to avoid extremely big DCD files). Inspired by John Stone's 'animatepdbs' script. Expanded to handle file masks (similar to 'ls' command) without specification of the first and last files in sequence (autodetect). For big file sequences can automatically wrap them into trajectory pieces by 'outFrames' frames number.
Usage: coordinates2dcd <filesPath> <fileNameFormat> <|fileType> <|outFrames> <|start> <|end>

COORs2DCDs - Similar to the previous script. This script finds all the files fitting into the filemask, e.g. "*.vel *.coor *.pdb" (search may be recursive into subfolders). Then it converts them individually into DCD format (one single-frame DCD per one file). It can (optionally) delete originals. Useful when you want in one step to free up some space, since DCD takes 2 time less space than the *coor or *.vel, and about 6 times less that PDB. Be careful with PDBs since DCD will retain only coordinates and will discard all other information (atom names, beta and occupancy fields etc.).

count_atoms_in_selection_of_trajectory_for_filelist - This script counts atoms within selection for all the frames of the trajectory and records results as a separate text files corresponding to the files in the filelist. Also script extracts 1 parameter value (e.g. Z coordinate) for every atom in selection for every timestep

count_h-bonded_water_bridges - This script counts water molecules which is binded with more than one other residue (i.e. functions like a bridge) within selection for all the frames of trajectory and records results as separate text files corresponding to the files in the filelist.

create_trajectory_from_residues - Script to align all the residues in the selection (suggesting all the residues have the same atoms number), sort by RMSD, and save them as a trajectory (one residue - one time frame. It imitates dynamics of the single residue based on the single multiresidue snapshot. For multiple timesteps it repeats the operation for every timestep and appends them all in one long DCD trajectory.

draw_channel_cylindrical_surface - Script to draw rotational (along z axis) surface, e.g. surface approximating average channel radius. It reads text file with 2 columns of data, separated by single spaces (z and radius), or 3 columns (z, radius, color). Color, if specified, should be integer from 17 to 1040. File should have 1st line with column headers (it is ignored). (|||screenshot), It was used in Sukharev and Anishkin, 2005

draw_triangulated_surface_from_file - Script to read and draw triangulated surface. It reads text file with 9 columns of data, containing coordinates of a triangle, separated by single spaces (x1 y1 z1 x2 y2 z2 x3 y3 z3). Useful when you have some surface calculated in the external program, e.g. Matlab, and want to overlap it exactly with the structure in VMD. (|||screenshot)

extract_all_frames_as_PDBs_for_filelist - This script extracts the selection of atoms for all the frames of trajectory as separate PDB files (one file per frame). Updates the selection every frame (in can have different number of atoms every timestep). Useful when you want to analyze the selections later in some external program, like Matlab.

extract_all_frames_H-bonds_as_XYZs_for_filelist - This script extracts coordinates of atoms forming an H-bond within selection for all the frames of the trajectory as separate XYZ (donor line, acceptor line, etc) files (one file for each entrance in the filelist). Useful for creation of hydrogen bonding maps (see Anishkin and Sukharev, 2004).

mark_non-channel_atoms_by_1_and_channel_by_-1__filelist -  Script for autodetection of the protein atoms on the outside-facing surface (lipid-facing surface of the membrane channel; atoms will be marked by 1 in occupancy field) and inside-facing surface (pore-facing surface of the channel or protein core; marked by -1). Channel is supposed to be oriented such that the direction normal to membrane plane will be along z axis. Can be used as one of the steps of hydration energy profile calculation. (|||screenshot)

radial_distribution_for_atoms_in_selections_of_trajectory_for_filelist - This script calculates the distance distribution for atoms within selections for all the frames of trajectory and records results as separate text files corresponding to the input files in filelist. Can be used for ion-'water oxygen' or water 'oxygen-hydrogen' etc. correlation function.

reposition_atoms_along_radius_and_average_multiple_selections - Script to reposition all the atoms in specified selections, rotating them around z axis so that they all align along the y axis, i.e. from {x y z} to {0 r z}, where r - radial distance from the atom to the z axis. Then a <smoothed> average is calculated and plotted as semitransparent spheres. (|||screenshot)

show_forces_as_arrows -  Script to estimate forces acting on harmonically restrained atoms in simulation. Supposing that one frame has coordinates of restraint targets, script compares these two frames of trajectory, calculates force acting on restrained atoms (according spring constants in the BETA field), puts the value into OCCUPANCY field and draws the color-coded force arrows. (|||screenshot)

summarize_namd_logs - Script to find files fitting into filemask, then find in every file lines with certain beginning, and extract patterned information from those lines.

Models  of E. Coli MscL in the closed, expanded and open states 
(based on the Dr. H. Robert Guy models (Sukharev et al., 2001) with N-terminal domain in the open state modified according to (Anishkin et al., 2003); PDB format)

PSF topology and DCD trajectory files of targeted energy minimization in vacuo between the closed and open states of MscL. It resembles the modeled trajectory of MscL gating and the gating pathways observed in all-atom molecular dynamics MscL simulations.

Resting MscS

Model of inactivated MscS