A tool to (currently) read DSN6, BRIX, and MRC/CCP4 crystallography and cryo-EM files and interpolate their density values onto a cartesian grid map as used by AutoDock software. The tool can output AD4 grid maps (default) or grid MRC files.
On most platforms only "make" should be needed. On macOS the compiler in the Makefile needs to be changed to clang++ to use Brew's version supporting OpenMP - otherwise -fopenmp needs to be taken out of the CXXFLAGS in the Makefile.
For direct Python compilation and installation (as above, we recommend LLVM from HomeBrew for macOS), from within your favorite python environment run make python.
For the installed Python version please run ./run_cryoXkit.py.
The standalone terminal tool CryoXKit needs parameters for the density map file and AD4 grid maps to modify or grid map center x, y, z coordinates, grid map x, y, z dimensions, and optionally grid spacing (default is 0.375 A), type of map to write (0 .. nothing, 1 .. AD4 grid map, 2 .. MRC grid map), as well as the modifier function type (0 .. none, 1 .. logistics) when only the modifier map is of interest:
./cryoXkit mapfile center_x center_y center_z x_dim y_dim z_dim (spacing [0.375]) (write [1 = AD4 map]) (modifier fxn [1 = logistics])
*or* for map modification (automatically excludes e, d, and H* maps):
./cryoXkit mapfile gridfile (spacing [0.375]) (modifier fxn [1 = logistics])
Once built to test everything works the following command can be used:
./cryoXkit example/*.dsn6 42.43 41.664 10.503 40 40 40
It should produce the grid map file 1d3g_2fofc.map in the ./example folder and similar output:
Reading map file [example/1d3g_2fofc.dsn6]
-> DSN6 endian-swapped, file size: 1728512
-> x_dim = 115, y_dim = 120, z_dim = 112
-> a_unit = 90.6, b_unit = 90.6, c_unit = 122.4
-> alpha = 90, beta = 90, gamma = 120
-> Fractional to cartesian conversion matrix:
90.6000 -45.3000 -0.0000
0 78.4619 -0.0000
0 0 122.4000
-> Cartesian to fractional conversion matrix:
0.0110 0.0064 0.0000
0 0.0127 -0.0000
0 0 0.0082
-> density unit cell range: (25.0768, 13.5440, -17.7846) A to (54.4678, 69.1212, 40.2769) A
-> density range: -2.581 to 12.665 (average: -0.029997 +/- 1.000289; median: -0.118788)
<- Finished reading densities, took 10.085 ms.
Interpolating density data for 40x40x40 grid (spacing: 0.375 A)
-> grid start: (34.930, 34.164, 3.003) A
-> grid size: (15.000, 15.000, 15.000) A
<- Finished interpolating densities to grid map points, took 1.228 ms.
Calculating median
-> range: -2.156 to 10.769 (median: -0.578)
<- Done, took 0.143 ms.
Adjusting density values using logistics function modifier (l: -3 kcal/mol, w: 2 kcal/mol, x0: 0.122)
<- Finished adjusting, took 0.908 ms.
Writing AD4 grid map file [example/1d3g_2fofc.map]
<- Finished writing, took 11 ms.
Done. Overall runtime was 23.8 ms.
For map conversions, the tool only requires the map file and the AD4 grid map files, an example is (note: this will modify the AD4 map files) to run ./cryoXkit example/1ac8/*.dsn6 example/1ac8/*.map:
Reading grid map files:
-> example/1ac8/protein.A.map
-> example/1ac8/protein.C.map
-> example/1ac8/protein.SA.map
-> example/1ac8/protein.N.map
<- Done, took 36.376 ms.
Reading map file [example/1ac8/1ac8_2fofc.dsn6]
-> DSN6 endian-swapped, file size: 369152
-> x_dim = 79, y_dim = 62, z_dim = 69
-> a_unit = 108, b_unit = 77.3, c_unit = 51.7875
-> alpha = 90, beta = 90, gamma = 90
-> Fractional to cartesian conversion matrix:
108.0000 -0.0000 -0.0000
0 77.3000 -0.0000
0 0 51.7875
-> Cartesian to fractional conversion matrix:
0.0093 0.0000 0.0000
0 0.0129 -0.0000
0 0 0.0193
-> density unit cell range: (-9.2571, 69.1240, 28.7708) A to (50.9143, 114.4635, 77.6813) A
-> density range: -3.681 to 11.902 (average: -0.030685 +/- 1.000417; median: -0.121865)
<- Finished reading densities, took 2.301 ms.
Interpolating density data for 60x60x60 grid (spacing: 0.375 A)
-> grid start: (20.674, 82.194, 36.674) A
-> grid size: (22.500, 22.500, 22.500) A
<- Finished interpolating densities to grid map points, took 3.682 ms.
Calculating median
-> range: -3.515 to 11.530 (median: -0.293)
<- Done, took 0.532 ms.
Adjusting density values using logistics function modifier (l: -3 kcal/mol, w: 2 kcal/mol, x0: 0.214)
<- Finished adjusting, took 2.79 ms.
Writing AD4 grid map file [example/1ac8/protein.N.map]
Writing AD4 grid map file [example/1ac8/protein.A.map]
Writing AD4 grid map file [example/1ac8/protein.C.map]
Writing AD4 grid map file [example/1ac8/protein.SA.map]
Done. Overall runtime was 88.1 ms.