DisVis is a Python package and command line tool to visualize and quantify the accessible interaction space of distance restrained binary biomolecular complexes. It performs a full and systematic 6 dimensional search of the three translational and rotational degrees of freedom to determine the number of complexes consistent with the restraints. In addition, it outputs the percentage of restraints being violated and a density that represents the center-of-mass position of the scanning chain corresponding to the highest number of consistent restraints at every position in space.
- Python 3.11+
- NumPy
- pyFFTW (FFTW3 bindings, for fast Fourier transforms)
- A C compiler (to build the extension modules)
NumPy and pyFFTW are installed automatically by pip; pyFFTW comes as a prebuilt package that includes FFTW3 for Linux, macOS and Windows.
For GPU hardware acceleration the following packages are also required
DisVis is best installed in a virtual environment. Open a terminal and type
git clone https://github.com/haddocking/disvis.git
cd disvis
python3 -m venv .venv
source .venv/bin/activate
pip install .
The build dependencies (NumPy and Cython) and the run-time dependencies (NumPy and pyFFTW) are installed automatically by pip. After installation, the command line tool disvis should be at your disposal.
For GPU acceleration, install the optional GPU requirements with
pip install '.[gpu]'
and build clFFT and gpyfft, which are not available from PyPI, as described in INSTALLATION.md.
Make sure git, the Python header files and a C compiler are available, e.g. on Debian/Ubuntu
sudo apt-get install git python3-dev python3-venv build-essential
If you are working on a Fedora system, use dnf and the python3-devel and gcc packages. Follow the general instructions above to install DisVis.
Install the Xcode command line tools, which provide git and a C compiler
xcode-select --install
and a recent Python 3, e.g. with brew
brew install python
Follow the general instructions above to install DisVis.
Install git for Windows, a Python 3 distribution, such as Anaconda, and the Microsoft C++ Build Tools. Follow the general instructions above to install DisVis.
The general pattern to invoke disvis is
disvis <pdb1> <pdb2> <distance-restraints-file>
where <pdb1> is the fixed chain, <pdb2> is the scanning chain and
<distance-restraints-file> is a text-file
containing the distance restraints in the following format
<chainid 1> <resid 1> <atomname 1> <chainid 2> <resid 2> <atomname 2> <mindis> <maxdis>
As an example
A 18 CA F 27 CB 10.0 20.0
This puts a distance restraint between the CA-atom of residue 18 of chain A of pdb1 and the CB-atom of residue 27 of chain F of pdb2 that should be longer than or equal to 10A and smaller than or equal to 20A. Comments can be added by starting the line with the pound sign (#) and empty lines are ignored.
To get a help screen with available options and explanation type
disvis --help
Some examples to get you started. To perform a 5.27 degree rotational search and store the results in the directory results/
disvis 1wcm_A.pdb 1wcm_E.pdb restraints.dat -a 5.27 -d results
Note that the directory is created if it doesn't exist.
To perform a 9.72 degree rotational search with 16 processors and a voxel spacing of 2A
disvis O14250.pdb Q9UT97.pdb restraints.dat -a 9.72 -p 16 -vs 2
To offload computations to the GPU (if the requirements are met) and increase the maximum allowed volume of clashes as well as the minimum required volume of interaction, and set the interaction radius to 2A
disvis 1wcm_A.pdb 1wcm_E.pdb restraints.dat -g -cv 6000 -iv 7000 -ir 2
To perform a grid occupancy analysis for complexes consistent with at least N
restraints, include the -oa or --occupancy-analysis flag to the command. By
default, the analysis is only performed on complexes consistent with
either all and all - 1 restraints. If you want to perform an occupancy
analysis for complexes consistent with a lower number of restraints, use the
-ic or --interaction-restraints-cutoff option, followed by the minimum
number of required consistent restraints. Thus the command
disvis 1wcm_A.pdb 1wcm_E.pdb restraints.dat -oa -ic 5
will make an occupancy grid for complexes consistent with at least 5 restraints, and higher.
Finally, to perform an interaction analysis to determine which residues
are most likely at the interface, the -is or --interaction-selection
options can be used with an additional file giving the residue numbers of the
receptor and ligand for which the interaction analysis will be performed. The
input file consists of two lines, where the two lines are a space separated
sequence of residue numbers for the receptor and ligand, respectively. As the
interaction analysis is particularly expensive, only complexes consistent with
all, or all - 1 are considered. To lower the barrier, the -ic option can
again be used. Also limit the selected residues to only the solvent accessible
ones. A simple example for the selection-file
1 2 3 4
101 302 888
This will select residue numbers 1, 2, 3, and 4 for the receptor, and 101, 302, and 888 for the ligand.
Standard disvis outputs 5 files:
- accessible_complexes.out: a text file containing the number of complexes consistent with a number of restraints.
- violations.out: a text file showing how often a specific restraint is violated for each number of consistent restraints. This helps in identifying which restraint is most likely a false-positive if any.
- accessible_interaction_space.mrc: a density file in MRC format. The density represents the center of mass of the scanning chain conforming to the maximum found consistent restraints at every position in space. The density can be inspected by opening it together with the fixed chain in a molecular viewer (UCSF Chimera is recommended for its easier manipulation of density data, but also PyMol works).
- z-score.out: a text file giving the Z-score for each restraint. The higher the score, the more likely the restraint is a false-positive. Z-scores above 1.0 are explicitly mentioned in the output.
- disvis.log: a log file showing all the parameters used, together with date and time indications.
If an occupancy and/or interaction analysis was requested, disvis also outputs the following files:
- occupancy_N.mrc: a volume file giving a normalized indication of how frequent a grid point is occupied by the ligand, where N indicates the minimal required number of consistent restraints that resulted in the occupancy grid.
- [receptor|ligand]_interactions.txt: a text file containing the average number of interactions per complex each selected residue made, for both the receptor and ligand molecule. Each column denotes the minimal number of consistent restraints of each complex for which interactions were counted.
To visualize the most contacted residues, write the average number of interactions into the B-factor column of the receptor or ligand PDB file
python scripts/interactions_to_bfactor.py receptor.pdb receptor_interactions.txt N
where N is one of the column numbers of the interaction file. This writes
receptor_interactions.pdb, which can be colored on B-factor, e.g. with
spectrum b, blue_red in PyMOL or color bfactor in ChimeraX.
If this software was useful to your research please cite us
Van Zundert, G.C.P. and Bonvin, A.M.J.J. (2015) DisVis: Visualizing and quantifying accessible interaction space of distance restrained biomolecular complexes. Bioinformatics 31, 3222-3224.
Apache License Version 2.0
The elements.py module is licenced under the MIT License, Copyright Christoph Gohlke.
| Operating System | CPU single | CPU multi | GPU |
|---|---|---|---|
| Linux | Yes | Yes | Yes |
| MacOSX | Yes | Yes | Yes |
| Windows | Yes | Fail | No |
The GPU version has been tested on: NVIDIA GeForce GTX 1080 Ti and RTX 6000 Ada for Linux, and Apple M2 Pro for macOS (and, with the earlier Python 2 version, NVIDIA GeForce GTX 680 and AMD Radeon HD 7730M for Linux)
Reference results and timings for the test cases, on CPUs and GPUs, are in
test-cases/README.md.
See CONTRIBUTING.md for the development setup, code style, tests and pull
requests.