CAVENV (CCP4: Supported Program)

NAME

cavenv - Visualise cavities in macromolecular structures

SYNOPSIS

cavenv xyzin foo_in.pdb mapout foo_out.map
[Keyworded input]

DESCRIPTION

CAVENV produces a CCP4 map from an input model structure, which is designed to help visualise cavities in the protein. By default, the program produces a "cavity" map in which each grid point is given a value equal to the distance of the closest atom, minus its Van der Waals radius, up to a maximum of <maxrad> (maximal probe radius to be tested). Thus the grid values are zero within the Van der Waals envelope of the protein. Outside this envelope, the value represents radius of the largest probe that access that grid point. In the middle of solvent regions, the grid value is that of the largest probe considered <maxrad>.

The program will also output an estimate of the percent protein and percent solvent in the volume covered by the generated map. Here, "protein" refers to the Van der Waals envelope of the atoms in the input model, and will include crystallographic waters unless they are specifically excluded. The "solvent" is the complement of the protein region, and thus larger than the volume accessible to the centre of a solvent probe. These percentages can only be compared to the value from a Matthews coefficient calculation if the output map covers a whole number of asymmetric units.

If one of the keywords ENVPROTEIN, ENVNCS or ENVSOLVENT is given, then a mask is produced instead of the cavity map.

INPUT AND OUTPUT FILES

The following input and output files are used by the program:

Input Files:

XYZIN
Coordinates of model of interest. The program will generate symmetry mates of the input coordinates automatically.

Output Files:

MAPOUT
Output map containing cavity map, or mask.

KEYWORDED INPUT

TITLE <title string>

Job title. Included in MAPOUT header.
Default is "From CAVENV".

RADMAX <maxrad>

Maximum probe radius to be tested in Angstrom.
Default is 3.0

RANGE <nfirst> <nlast>

Residue range of atoms to be included from XYZIN. This applies to all chains.
Default range is 1 to 10000.

EXCLUDE <atomname>

Atoms to be excluded from XYZIN, e.g. "EXCLUDE NZ". Several EXCLUDE cards may be given (up to a maximum number which is currently 150).

CELL <a> <b> <c> [ <alpha> <beta> <gamma> ]

Input cell parameters explicitly. If omitted, program will try to obtain cell parameters from XYZIN.

SYMM [<spacegroup number> | <spacegroup name> | <symmetry operations> | OFF]

Input spacegroup explicitly. If omitted, program will try to obtain spacegroup from XYZIN.

The spacegroup symmetry operators, together with lattice translations up to one unit cell in any direction, are used to generate symmetry mates of the atoms in XYZIN that lie within the limits of the output map. If the input coordinates are in a wildly different location from the desired map limits, then some relevant coordinates may not be generated.

If the subkeyword OFF is given, then no symmetry or lattive translations are applied.

AXIS <fast axis> <medium axis> <slow axis>

Specify the axis order for the output map, where each axis is one of "X", "Y" or "Z".
Default is "AXIS X Y Z".

GRID <nx> <ny> <nz>

Number of sampling divisions along whole cell edges.
Default is such as to give grid spacing of 0.5 A.

XYZLIM <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

Range of unit cell to be included in output map. <xmin> <xmax> etc. are minimum and maximum grid numbers along each cell edge.
Default is to include entire unit cell.

ENVPROTEIN

Instead of the default cavity map, MAPOUT will contain a protein mask with 1's within the protein region and 0's in the solvent region. The solvent region is defined as the volume accessible by a probe of radius <maxrad> (see RADMAX keyword). Thus the solvent region corresponds to the flat central region of the cavity map, when the same value of <maxrad> is used.

ENVNCS <numncs>

As ENVPROTEIN, but masks will be generated for <numncs> NCS-related molecules. This card should be followed by 3 x <numncs> records specifying the NCS operators. Each record consists of 3 elements of the rotation matrix and one element of the translation. The first group of three records will usually represent the identity:

1.0 0.0 0.0 0.0
0.0 1.0 0.0 0.0
0.0 0.0 1.0 0.0

ENVSOLVENT

Instead of the default cavity map, MAPOUT will contain a solvent mask with 1's within the solvent region and 0's in the protein region. The solvent region is defined as the volume accessible by a probe of radius <maxrad> (see RADMAX keyword). Thus the solvent region corresponds to the flat central region of the cavity map, when the same value of <maxrad> is used.

END

End of the keyword list

EXAMPLES

Runnable examples using rnase data

Other examples

[job example (unix)]

cavenv xyzin model.pdb mapout output.map << eof
range 1 2000  		   ! include this residue range
radmax 3.0			   ! add 3.0 Angstroem to R_vdw
TITLE probe sizes < 3 Angstroem  ! title for cavity map or envelope
CELL 100. 100. 100. 90. 90. 90.  ! unit cell (can be artificial)
AXIS X Y Z 		   ! fast, medium and slow map index
GRID 200 200 200		   ! Ngrid along A/B/C for unit cell
XYZLIM 46 102 58 144 166 224     ! grid limits along A/B/C
SYMMETRY 1			   ! space group
ENVNCS 6			   ! make envelope for a hexamer
1.0 0.0 0.0 0.0		   !
0.0 1.0 0.0 0.0		   ! 1st ncs operation
0.0 0.0 1.0 0.0		   !
-0.496382    0.868067   -0.008077	   21.3054 !
-0.868089   -0.496407   -0.001331	   39.5577 ! 2nd ncs operation
-0.005165    0.006350    0.999966	   44.4143 !
-1.000000   -0.000038    0.000297	   44.4809 !
 0.000039   -1.000000    0.000687	   92.5910 ! 3rd ncs operation
 0.000297    0.000687    1.000000	   66.5566 !
-0.498075   -0.867075    0.010130	   44.8044 !
 0.867133   -0.498059    0.004165	    1.1216 ! 4th ncs operation
 0.001434    0.010859    0.999940	   88.5292 !
 0.498336    0.866924   -0.010155	   -0.3177 !
-0.866981    0.498328   -0.003483	   91.4965 ! 5th ncs operation
 0.002041    0.010540    0.999942	   21.9734 !
 0.496579   -0.867951    0.008414	   23.1853 !
 0.867971    0.496611    0.002098	   53.0822 ! 6th ncs operation
-0.005999    0.006261    0.999962	  110.9757 !
eof

Bugs

The main memory requirement is holding the map in memory. The program is currently dimensioned to hold a maximal map size of 3375000 (150*150*150) grid points. If this is too large for your system, then you need to change the value of NMAP in 1 PARAMETER statement in the source code, and recompile.

SEE ALSO

areaimol - Analyse solvent accessible areas

REFERENCES

  1. A. Volbeda, private communication or with reference (in french): Anne Volbeda, Speleologie des hydrogenases a nickel et a fer. In: "Les Ecoles Physique et Chimie du Vivant, numero 1 - avril 1999, Analyse de l'organisation tridimensionnelle des proteines", pp 47-52.

Other examples using CAVENV:

  1. T. I. Doukov, T. M. Iverson, J. Seravalli, S. W. Ragsdale, C. L. Drennan (2002) Science 298 567 - 572
    "... putative channel for CO as calculated by program CAVENV..."

AUTHORS

ANNE VOLBEDA, IBS/LCCP GRENOBLE
CCP4 version - Martyn Winn