Correlation-Based Docking Tutorial
This tutorial teaches new users the application of the exhaustive 6D seach and FFT-accelerated docking program colores for rigid-body docking. Colores provides options for contour-based enhancement of the fitting contrast by means of a Laplacian filter that can also be turned off if desired. The results of this tutorial can be compared to solutions distributed with the tutorial software. More documentation is available in the user guide , on the methodology page, and in the published articles .
Content:
Download and Installation

First, follow these registration and download steps (each Situs tutorial is separate and must be downloaded individually)!

Then, return to this page.

In addition to the executables, the Situs_2.7.2_correlation_tutorial/bin directory contains three data files and an executable shell script:

  • 0_monomer.pdb: Atomic (carbon alpha) coordinates of one of the monomers of RecA from PDB entry 2REC.
  • 0_hexamer.situs: Simulated EM map (Situs format) at 15Å resolution of the RecA hexamer (PDB entry 2REC).
  • 0_hexamer_reference.pdb: For validating purposes, PDB entry 2REC.
  • run_tutorial.bash: Bash shell script containing all commands of this tutorial (actually, there is only one shell command here, the VMD scripts shown below are more important in this tutorial).

The user can compare all generated files to the files in the "solutions" directory. Here is an overfiew of the fitting scenario. 
In the following, we will use the first two files for docking:

Data Flow and Design

The series of steps and the programs that are required to use colores for the docking of an atomic-resolution structure to low-resolution data are shown schematically in the following figure. Detailed program explanations are given in the Situs user guide .

Schematic diagram of colores related routines. Major Situs components (light blue) are classified by their functionality. The main work flow is indicated by brown arrows, and the optional inspection of Euler angles in dark blue arrows. The visualization (orange) for the rendering of the models requires a molecular graphics viewer (we use here the VMD graphics program, Chimera and Sculptor also support Situs format).


Standard EM formats are supported and are converted to cubic lattices in Situs format. This is done with the map2map utility. Subsequently, the data is inspected and, if necessary, prepared for the fitting using a variety of visualization and analysis tools.
All Situs tools require one volume and one PDB structure for the fitting. Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa, to allow docking of maps to maps or structures to structures. The resulting docked complex can be inspected in the graphics program. Also, if a subset of Euler angles is chosen these can be inspected after conversion into PDB format with the eul2pdb tool.

Running colores

For this particular docking case it will be sufficient to perform a reduced angular search (sampled at 20°-> option -deg 20) to restore the original atomic structure that we used to generate the 15Å simulated EM map (target resolution 15Å -> option -res 15). After the exhaustive search is done, the best 6 on-lattice maxima (option -explor 6) will be refined (off-lattice) using Powell optimization. Here is the command that runs this search:

./colores 0_hexamer.situs 0_monomer.pdb -res 15.0 -deg 20 -explor 6

When starting the program (by default as a single processor run), it will first display the user assigned and default assigned options. Here you can check if all the input options that you requested were understood, and if you agree with the default assignment of the orther options (the user assigned options are marked in blue). For example, at
15Å resolution the program uses by default the Laplacian filter that enhances the fitting contrast, and assigns a density threshold of 0.0, i.e. only positive values will be considered:

colores> Options read:
colores> Target resolution 15.000
<== -res 15
colores> Resolution anisotropy 1.000
colores> Low-resolution map cutoff 0.000
colores> Laplacian filtered correlation
colores> FFT grid size expansion factor 0.200 (thickness of additional zero layer as fraction of map dimensions)
colores> Euler angles generation using Proportional method
colores> Angular sampling accuracy 20.000
<== -deg 20
colores> Euler angle range: [0.000:360.000] [0.000:180.000] [0.000:360.000]
colores> Sculptor mode OFF
colores> Number of best fits explored  6
<== -explor 6
colores> Original peak search by sort and filter
colores> Powell maximization ON
colores> Powell tolerance 1.00E-06  Max iterations 25
colores> Powell trans & rot initial step sizes set to default values
colores> Powell correlation algorithm determined automatically
colores> Peak sharpness estimation ON
colores> Number of SMP processors requested: 1


Then the input files will be read. You can check if the map parameters, as well as the size of the atomic structure, are as expected:


colores> Processing low-resolution map.
lib_vio> Situs formatted map file 0_hexamer.situs - Header information:
lib_vio> Columns, rows, and sections: x=1-43, y=1-41, z=1-29
lib_vio> 3D coordinates of first voxel: (-84.000000,-80.000000,-68.000000)
lib_vio> Voxel size in Angstrom: 4.000000
lib_vio> Reading density data...
lib_vio> Volumetric data read from file 0_hexamer.situs
lib_vwk> Setting density values below 0.000000 to zero.
lib_vwk> Remaining occupied volume: 51127 voxels.
lib_vwk> Map size changed from 43 x 41 x 29 to 37 x 35 x 23.
lib_vwk> New map origin (coord of first voxel): (-72.000,-68.000,-56.000)
lib_vwk> Map density info: max 5.881478, min 0.000000, ave 0.709373, sig 1.280587.
_____________________________________________________________________________
colores> Processing atomic structure.
lib_pio> 303 atoms read.
colores> Geometric center: -12.369 -36.951 -9.252, radius: 40.526 Angstrom


Next, the Gaussian filter that is used for lowering the resolution of the atomic structure, and the Laplacian filter that is used to add the contour information to the fitting criterion, are generated:


lib_vwk> Generating Gaussian kernel with 7^3 = 343 voxels.
lib_vwk> Generating Gaussian kernel with 11^3 = 1331 voxels.
lib_vwk> Generating Laplacian kernel with 3^3 = 27 voxels.
lib_vwk> Generating kernel with 9^3 = 729 voxels.
lib_vwk> Map size expanded from 37 x 35 x 23 to 61 x 57 x 41 by zero-padding.
lib_vwk> New map origin (coord of first voxel): (-120.000,-112.000,-92.000)
colores> Identifying inside or buried voxels and creating flipped mask...
colores> Found 11957 inside or buried voxels (out of a total of 142557).
colores> Identifying inside or buried voxels...
colores> Found 11957 inside or buried voxels (out of a total of 142557).
colores> Memory allocation for FFT.
colores> FFT planning...

As a test, the correlation is calculated with the probe structure centered in target density map. In this case, since the low resolution map has a "hole" in the center, the Laplacian correlation yields negative values:

colores> Testing the maps and correlations.
colores> Projecting probe structure to lattice...
colores> Low-pass-filtering probe map...
colores> Target and probe maps:
lib_vwk> Map density info: max 5.881478, min 0.000000, ave 0.148212, sig 0.675602.
lib_vwk> Map density info: max 5.614532, min 0.000000, ave 0.025529, sig 0.279312.
colores> Projecting probe structure to lattice...
colores> Applying filters to target and probe maps...
lib_vwk> Relaxing 5 voxel thick shell about thresholded density...
colores> Normalizing target and probe maps...
colores> Target and probe maps:
lib_vwk> Map density info: max 9.253166, min -12.816330, ave -0.000063, sig 0.560102.
lib_vwk> Map density info: max 16.796933, min -30.926755, ave -0.004420, sig 0.472828.
colores> Writing target and probe maps for inspection or debugging...
lib_vio> Writing density data...
lib_vio> Volumetric data written to file col_hi_fil.sit
lib_vio> File col_hi_fil.sit - Header information:
lib_vio> Columns, rows, and sections: x=1-61, y=1-57, z=1-41
lib_vio> 3D coordinates of first voxel: (-120.000000,-112.000000,-92.000000)
lib_vio> Voxel size in Angstrom: 4.000000
lib_vio> Writing density data...
lib_vio> Volumetric data written to file col_lo_fil.sit
lib_vio> File col_lo_fil.sit - Header information:
lib_vio> Columns, rows, and sections: x=1-61, y=1-57, z=1-41
lib_vio> 3D coordinates of first voxel: (-120.000000,-112.000000,-92.000000)
lib_vio> Voxel size in Angstrom: 4.000000
colores> Computing correlation between maps in direct space...
colores> Correlation with structure centered in density map:  -4.2820480E-02
colores> Computing correlation in Fourier space...
colores> FFT correlation with structure centered in density map:  -4.2820480E-02


Now the uniform distribution of the Euler angles that covers the rotational search space is computed. The triplets of Euler angles are saved in the file col_eulers.dat. This file can be edited or can be used again at other times when you perform a search with idenical sampling:


colores> Getting Euler angles.
lib_eul> Proportional Euler angles distribution, total number 1908 (delta = 20.000000 deg.)
colores> Total number of orientations sampled: 1908
colores> Euler angles saved in file col_eulers.dat.

Here follows the system-dependent time estimate for the 6D on-lattice search:

colores> Time of one FFT calculation: 23.093000 ms
colores> Average time spent on each rotation: 47.894200 ms
colores> Estimated time for full 6D (on-lattice) search: 0 h 1 m 31 s
colores> Off-lattice Powell optimization will take significant extra time.

Then the 6D on-lattice search is performed. During this search a progressive information about the best translational fit for each orientation is written to the file col_rotate.log. A progress bar keeps you informed:

colores> Starting 6D on-lattice search with 3D FFT scan of Euler angles.
colores> Searching using 1 processors
colores> |##################################################|   1908/1908 | 100% done
colores> Actual time spent on 6D on-lattice search: 0 h 1 m 33 s

Next follows a peak search of the maximal correlation values, after which the program enters the Powell off-lattice optimization of the selected (-explor) 6 highest scoring maxima:

colores> Translation function peak detection.
colores> Peak filter contrast: maximum 0.924312, sigma 0.064743
colores> Contrast threshold: 0.129486, candidate peaks: 185
colores> Found 72 non-redundant peaks.
_____________________________________________________________________________
colores> Off-lattice search (Powell's optimization method).
colores> Determining most efficient correlation algorithm based on convergence and time...
colores>    Original algorithm: Correlation = -0.01498504  Time = 1.498000 ms
colores>    Masked algorithm:   Correlation = -0.01506857  Time = 1.376500 ms
colores>    One-step algorithm: Correlation = -0.01498504  Time = 1.105000 ms
colores> Using one-step correlation function.
colores> Shown are: offset (in A) from reference center (2.000,2.000,-10.000),
colores> Euler angles (in degrees), and correlation value.
colores>
colores> Performing optimizations...
colores>
colores> Powell optimization for score maximum no.  1.
colores>   X       Y       Z       Psi     Theta   Phi      Correlation
colores>  24.000 -32.000   0.000   0.000   0.000 300.000    3.8181654E-01 Initial
colores>  23.718 -31.115   0.621  -0.795   0.132 300.007    3.9282045E-01 1
colores>  23.888 -31.124   0.635  -0.814   0.160 300.008    3.9303528E-01 2
colores>  23.887 -31.124   0.633  -0.814   0.160 300.008    3.9303573E-01 3
colores>  23.887 -31.124   0.633  -0.814   0.160 300.008    3.9303573E-01 4
colores>  23.887 -31.124   0.633 359.186   0.160 300.008    3.9303573E-01 Final
colores>
colores> Powell optimization for score maximum no.  2.
colores>   X       Y       Z       Psi     Theta   Phi      Correlation
colores> -28.000  28.000   0.000   0.000   0.000 120.000    3.8181517E-01 Initial
colores> -27.718  27.115   0.621  -0.795  -0.132 120.007    3.9281792E-01 1
colores> -27.888  27.124   0.635  -0.814  -0.160 120.008    3.9303254E-01 2
colores> -27.887  27.124   0.633  -0.814  -0.160 120.008    3.9303300E-01 3
colores> -27.887  27.124   0.633  -0.814  -0.161 120.008    3.9303301E-01 4
colores> -27.887  27.124   0.633 179.186   0.161 300.008    3.9303301E-01 Final
colores>
colores> Powell optimization for score maximum no.  3.
colores>   X       Y       Z       Psi     Theta   Phi      Correlation
colores> -40.000  -8.000   0.000   0.000   0.000  60.000    3.6045063E-01 Initial
colores> -40.280  -9.766   0.644  -0.345  -0.085  60.000    3.8385660E-01 1
colores> -40.330  -9.824   0.643  -0.282  -0.052  60.000    3.8393576E-01 2
colores> -40.338  -9.814   0.644  -0.253  -0.047  60.000    3.8394305E-01 3
colores> -40.366  -9.796   0.647  -0.152  -0.031  60.000    3.8396217E-01 4
colores> -40.367  -9.795   0.647  -0.149  -0.031  60.000    3.8396229E-01 5
colores> -40.367  -9.795   0.647 179.851   0.031 240.000    3.8396229E-01 Final
colores>
colores> Powell optimization for score maximum no.  4.
colores>   X       Y       Z       Psi     Theta   Phi      Correlation
colores>  36.000   4.000   0.000   0.000   0.000 240.000    3.6044767E-01 Initial
colores>  36.280   5.766   0.644  -0.345   0.085 240.000    3.8385590E-01 1
colores>  36.330   5.824   0.643  -0.282   0.052 240.000    3.8393511E-01 2
colores>  36.338   5.814   0.644  -0.254   0.047 240.000    3.8394234E-01 3
colores>  36.367   5.796   0.647  -0.151   0.031 240.000    3.8396147E-01 4
colores>  36.367   5.795   0.647  -0.149   0.031 240.000    3.8396158E-01 5
colores>  36.367   5.795   0.647 359.851   0.031 240.000    3.8396158E-01 Final
colores>
colores> Powell optimization for score maximum no.  5.
colores>   X       Y       Z       Psi     Theta   Phi      Correlation
colores> -16.000 -40.000   0.000   0.000   0.000   0.000    3.5694334E-01 Initial
colores> -14.184 -38.973   0.621  -0.535  -0.365  -0.088    3.9651018E-01 1
colores> -14.301 -39.025   0.653  -0.535  -0.463  -0.141    3.9669580E-01 2
colores> -14.296 -39.054   0.662  -0.535  -0.521  -0.158    3.9670773E-01 3
colores> -14.292 -39.075   0.664  -0.535  -0.531  -0.171    3.9671264E-01 4
colores> -14.292 -39.075   0.666  -0.535  -0.533  -0.171    3.9671285E-01 5
colores> -14.292 -39.075   0.666 179.465   0.533 179.829    3.9671285E-01 Final
colores>
colores> Powell optimization for score maximum no.  6.
colores>   X       Y       Z       Psi     Theta   Phi      Correlation
colores>  12.000  36.000   0.000   0.000   0.000 180.000    3.5694033E-01 Initial
colores>  10.184  34.973   0.621  -0.535   0.365 179.912    3.9650980E-01 1
colores>  10.301  35.025   0.653  -0.535   0.463 179.859    3.9669525E-01 2
colores>  10.296  35.053   0.662  -0.535   0.521 179.841    3.9670722E-01 3
colores>  10.292  35.075   0.664  -0.535   0.532 179.829    3.9671214E-01 4
colores>  10.292  35.076   0.666  -0.534   0.533 179.828    3.9671237E-01 5
colores>  10.292  35.076   0.666 359.466   0.533 179.828    3.9671237E-01 Final
colores>
colores> Powell optimization time (6 runs): 10.687460 s


As we will see later, the six saved fits correspond to the symmetry-related placement of the monomer into the hexameric density. The peak sharpness is estimated for every solution (can be turned off) and the found highest scoring results are written to PDB files:

colores> Renormalizing correlation values by highest score.
colores> Writing translation function lattice to Situs file.
lib_vio> Writing density data...
lib_vio> Volumetric data written in Situs format to file col_trans.sit
lib_vio> Situs formatted map file col_trans.sit - Header information:
lib_vio> Columns, rows, and sections: x=1-61, y=1-57, z=1-41
lib_vio> 3D coordinates of first voxel: (-120.000000,-112.000000,-92.000000)
lib_vio> Voxel size in Angstrom: 4.000000
colores> Writing translation function lattice information to log file.
_____________________________________________________________________________
colores> Saving the best results.
colores> Estimating peak sharpness and writing best fit no.   1 to file col_best_001.pdb.
colores> Estimating peak sharpness and writing best fit no.   2 to file col_best_002.pdb.
colores> Estimating peak sharpness and writing best fit no.   3 to file col_best_003.pdb.
colores> Estimating peak sharpness and writing best fit no.   4 to file col_best_004.pdb.
colores> Estimating peak sharpness and writing best fit no.   5 to file col_best_005.pdb.
colores> Estimating peak sharpness and writing best fit no.   6 to file col_best_006.pdb.

Finally, in addion of the output file coordinates a number of output log files (described in the next section) are saved:

colores> Output files:
   col_best*.pdb      => Best docking results in PDB format with info in header
   col_eulers.dat     => colores-readable list of Euler angles
   col_rotate.log     => Rotation function (unnormalized) log file
   col_trans.log      => Translation function (norm. by best fit) log file
   col_trans.sit      => Translation function (norm. by best fit) in Situs format
   col_lo_fil.sit     => Filtered target volume in Situs format, just prior to correlation calculation
   col_hi_fil.sit     => Filtered (and centered) probe structure in Situs format, just prior to correlation calculation
   col_powell.log     => Powell optimization log file

Inspecting the Results

In this section, we inspect with
VMD how well the docked structures fit into the map. For convenience, the following VMD commands can be pasted directly into the VMD command shell:

vmd shell commands:

mol load situs 0_hexamer.situs
mol load pdb col_best_001.pdb
mol load pdb col_best_002.pdb
mol load pdb col_best_003.pdb
mol load pdb col_best_004.pdb
mol load pdb col_best_005.pdb
mol load pdb col_best_006.pdb
mol top 0
rotate stop
display resetview
display projection orthographic
mol modstyle 0 0 Isosurface 1 0 0 1 2 1
mol modstyle 0 1 Trace 0.3 32
mol modstyle 0 2 Trace 0.3 32
mol modstyle 0 3 Trace 0.3 32
mol modstyle 0 4 Trace 0.3 32
mol modstyle 0 5 Trace 0.3 32
mol modstyle 0 6 Trace 0.3 32
mol modcolor 0 0 ColorID 0
mol modcolor 0 1 ColorID 3
mol modcolor 0 2 ColorID 3
mol modcolor 0 3 ColorID 3
mol modcolor 0 4 ColorID 3
mol modcolor 0 5 ColorID 3
mol modcolor 0 6 ColorID 3


Don't forget to hit "enter" after the last line! Do not exit VMD yet.

Now we compare the six docked monomers with the original hexameric structure (0_hexamer_reference.pdb) that we used for generating the 15Å resolution map (note that we toggle off the isocontour wireframe for a better display):

vmd shell commands:

mol off 0
mol load pdb 0_hexamer_reference.pdb
mol modstyle 0 7 Trace 0.30 32.0



In this picture you can see how the best docking results (in orange) are practically identical to the original structure (in cyan). In fact the average distance between the docked monomers and their corresponding subunits in the original structure is <<1Å rmsd.

Don't forget to hit "enter" after the last line! Do not exit VMD yet.

You can also inspect the maximal translational correlation values found in the on-lattice search (the so-called translation function) by using the map col_trans.sit. This Situs format file contains the 3D correlation values (normalized to the maximum value) as a function of translation only (the rotations have been projected out by using the optimum orientation for each voxel).

As we did before, paste the following commands in the VMD command shell:


vmd shell commands:

mol off 1
mol off 2
mol off 3
mol off 4
mol off 5
mol off 6
mol off 7
mol on 0
mol load situs col_trans.sit
mol modstyle 0 8 Isosurface 0.4 0 0 0 1 1
mol modcolor 0 8 ColorID 4
mol top 0
rotate stop
display projection orthographic
display resetview

On the right you can see the VMD display. The higher correlational values are represented in yellow. These regions correspond roughly to the centers of mass of the six subunits that underlie the simulated map (wireframe in blue).

Alternatively, you can inspect the translation function with voledit: To make a 2D representation of a slice with an external plotting program, you can export the correlation values and grid indices of a given slice to a file.

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