This was my personal git repository for the voltool plugin of VMD
while I worked for the Theoretical and Computational Biophysics Group at the University of Illinois Urbana-Champaign.
voltool is a set of utility methods for manipulating the volumetric data (density maps) used by the mdff plugin of VMD.
The molecular dynamics flexible fitting (MDFF) method can be used to flexibly fit atomic structures into density maps (usually Cryo-EM, or
low-resolution X-ray crystallography for xMDFF). The method consists of adding external forces proportional to the gradient of the density map
into a molecular dynamics (MD) simulation of the atomic structure.
This version of voltool represents a large overhaul of an older plugin to improve computational efficiency and add many new features including
a fast rigid-body fitting method.
I no longer work at UIUC or with current voltool or mdff development, so this repo is now archived. For current VMD related information please
see the official site
New rigid body fitting and volumetric data utilities for VMD.
Usage: voltool <command> [args...]
Commands:
map operations using an atomic structure:
fit -- rigid body fitting
cc -- calculates the cross-correlation coefficient between a map and structure
sim -- creates a simulated map from an atomic structure
operations on one map:
com -- get center of mass of density
moveto -- move density com to a specified coordinate
move -- apply specified 4x4 transformation matrix to density
trim -- trim edges of a density
crop -- crop density to values given in coordinate space
clamp -- clamp out of range voxel values
smult -- multiply every voxel by a scaling factor
sadd -- add a scaling factor to every voxel
range -- fit voxel values to a given range
downsample -- downsample by x2 (x8 total reduction)
supersample -- supersample by x2 (x8 total increase)
sigma -- transform map to sigma scale
binmask -- make a binary mask of the map
smooth -- 3D gaussian blur
operations on two maps:
add -- add two maps together
diff -- subtract map2 from map1
mult -- multiply map1 and map2
avg -- average two input maps into one
correlate -- calculates the cross-correlation coefficient between two maps