VISDEM 1.2 (2025)

VISDEM 1.2 is a cryo‑EM density map sharpening tool developed by Gunnar F. Schröder, Michaela Spiegel, and Amudha Duraisamy. It estimates the underlying atomic distribution of a protein from the density map and computes the corresponding radially averaged structure factor and density histogram. These calculated profiles are then used to adjust the input map’s spectrum and histogram, enhancing map clarity. VISDEM 1.2 also supports the application of helical symmetry during the atomic distribution estimation.

Reference

M. Spiegel, A.K. Duraisamy, and G.F. Schröder. Improving the Visualisation of Cryo-EM Density Reconstructions
J.Struct.Biol. (2015), 191(2):207-213

Requirements

• A C compiler (GCC is recommended)
• FFTW3 library
• GNU Make

Building

Clone the repository and build the program by running:

make

This will produce an executable named visdem.

Usage

./visdem --input <input_map.mrc> --mass <mass in kDa> --resolution <cutoff in Å> --output <output_map.mrc> [--threshold <value>] [--rise <value> --twist <value>]

Command-Line Options

• -i, --input
  Input MRC map file.

• -o, --output
  Output MRC map file.

• -m, --mass
  Particle mass in kilodaltons (kDa).

• -r, --resolution
  Resolution cutoff in Å.

• -t, --threshold
  (Optional) Density threshold.

• --rise
  (Optional) Rise parameter for helical symmetry.

• --twist
  (Optional) Twist parameter for helical symmetry.

You can either just provide the mass, then the corresponding density threshold will be estimated, or you just provide the threshold, then the corresponding mass (and number of atoms) will be estimated, or you provide mass and threshold, then the number of atoms derived from the mass will be placed into the volume defined by the density threshold.

Example

To run the program with helical symmetry using a rise of 4.75 Å and a twist of -1.2°:

./visdem -i map.mrc -m 400 -r 2.5 -o sharpened.mrc --rise 4.75 --twist -1.2

If no threshold is provided, the program will compute one automatically from volume based on the provided mass.

License

This project is licensed under the GNU General Public License (GPL) version 3. See the LICENSE file for details.

Acknowledgments

VISDEM 1.2 (2025) is developed by Gunnar F. Schröder, Michaela Spiegel, and Amudha Duraisamy.