CAVENV (CCP4: Supported Program)
NAME
cavenv
- Visualise cavities in macromolecular structures
SYNOPSIS
cavenv xyzin
foo_in.pdb
mapout
foo_out.map
[Keyworded input]
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".
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
- cavenv.exam
Simple example of producing a cavity map from the rnase model coordinates.
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
- 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:
- 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