AREAIMOL (CCP4: Supported Program)

NAME

SYNOPSIS

DESCRIPTION

AREAIMOL finds the solvent accessible area of atoms in a PDB coordinate file, and summarises the accessible area by residue, by chain and for the whole molecule. It will also attempt to identify isolated areas of surface (which could be cavities either within the molecule, or formed as a result of intermolecular contacts). It is capable of excluding specified residues from the calculations, and of generating symmetry related molecules. It can also be used to compare accessible area and analyse area differences. Accessible areas (or area differences) for individual atoms can be written to a pseudo-PDB output file

This is an extensively revised version of the old AREAIMOL program which now also incorporates the functions of DIFFAREA, RESAREA and WATERAREA. The flexibility of the area calculation has been extended by the addition of new keywords PROBE (sets probe radius), PNTDEN (sets precision of area calculation) and ATOM (allows new atom types to be defined).

KEYWORDED INPUT

The keywords are spilt into three groups:

Main keywords which control the type of calculation

DIFFMODE, MODE, SMODE, SYMMETRY, TRANS

Secondary keywords which control parameters within the calculation

ATOM, EXCLUDE, MATCHUP, PNTDEN, PROBE

Auxiliary keywords

VERBOSE, OUTPUT, END

MAIN KEYWORDS

DIFFMODE OFF | IMOL | WATER | COMPARE

Subkeywords:

OFF [default]

This corresponds to the function of the original AREAIMOL program. A single input file is required and a single accessible area calculation and analysis is performed.

IMOL

This mode analyses the differences in accessible areas of a molecule due to different intermolecular contacts (generated from different sets of symmetry operators and/or lattice translations).

WATERS

This mode analyses the differences in accessible area for the waters in a molecule depending on whether they are treated as solvent or as protein.

COMPARE

This mode is used to analyse the area differences for atoms and residues which are common between molecules held in two different files (XYZIN and XYZIN2).

MODE ALL | NOHOH | HOH | HOHALL

Subkeywords:

NOHOH [default]

All waters (residue type HOH or WAT) are ignored.

HOH

The accessible area will only be calculated for waters (HOH or WAT), treating other waters as solvent. Only waters will be analysed.

HOHALL

As HOH, but waters are treated as protein, and consequently more waters will have low solvent accessiblity.

ALL

Calculate accessible area for all atoms, including waters if present in file. Water atoms are treated as solvent when calculating accessible area.
Warning: waters may have large accessible area assigned in this MODE, leading to unrealistically inflated estimates of the total accessible area. Check the output carefully.

SMODE IMOL | OFF

Subkeywords:

IMOL

Account for intermolecular contacts by generating symmetry related molecules from coordinates in Brookhaven file before calculating accessible areas, using symmetry operators supplied by the SYMMETRY keyword. (The TRANS keyword can also be used, to generate molecules related by lattice translation symmetry.)

OFF [default]

Symmetry related atoms will not be generated and intermolecular contacts are not accounted for.

SYMMETRY <space-group name | space-group number | symmetry operators>

If the SYMMETRY keyword is omitted when SMODE has been specified as IMOL then the program will generate symmetry related molecules assuming P1 symmetry (essentially, lattice translations only). If SMODE is OFF then the SYMMETRY keyword is optional.

Under DIFFMODE IMOL a second SYMMETRY keyword is neccessary, to specify the symmetry operators required for the second area calculation (see below).

Note that unlike previous versions of the program, it is no longer necessary to manually exclude the identity operation when entering symmetry operations. The identity is implicity assumed. If the identity is the only operation that has been entered (or if P1 symmetry is specified) then a warning may appear, but this can be ignored (unless you are not in P1 symmetry).

TRANS [ NONE | 1 | 2 | BOTH ]

TRANSlation keyword. This causes the program to generate additional symmetry-related molecules by applying 125 translations made up from linear combinations of the primitive lattice vectors (+/-2 lattice vectors in each direction). Combining these with the spacegroup operators via the SYMMETRY keyword will generate the crystal lattice.

Only takes effect if DIFFMODE IMOL or SMODE IMOL have been specified.

Subkeywords for DIFFMODE IMOL:

1 (or 2)

Apply the translation vectors on the first (or second) area calculation only.

BOTH

Apply the translations on both the first and the second area calculation.

NONE

[Default] Do not apply any translations.

For SMODE IMOL, NONE turns off the translations [default] and TRANS on its own is sufficient to switch them on.

Secondary Keywords

ATOM <name> <no> <radius>

If both <name> and <no> match those belonging to an atom already in the list then its Van der Waal radius will be changed to <radius>. If only one of either match, then the program ignores that occurance of the ATOM keyword and the radius will remain unchanged.

AREAIMOL assumes a single radius for each element, and only recognises a limited number of different elements. Unknown atom types (i.e. those not in AREAIMOL's internal database) will be asigned the default radius of 1.8 A. The list of recognised atoms is:

       Name  Atomic no. VdW rad. (A)
       -----------------------------
         C        6        1.80
         N        7        1.65
         O        8        1.60
        MG       12        1.60
         S       16        1.85
         P       15        1.90
        CL       17        1.80
        CO       27        1.80

EXCLUDE <residue1> <residue1> ...

Any number of specified residue names can appear together after a single EXCLUDE, separated by a space (eg EXCLUDE PRO ARG GLY). The EXCLUDE keyword can also be repeated any number of times with one or more specified residue names.

There is a maximum number of excluded residues which is set inside the program (currently 30). If there are more than this limit then extra names will not be recorded. Names entered in lower case will automatically be converted to uppercase. Note also that the program does not check that the entries given are valid residue names, or if any are repeated.

In DIFFMODE COMPARE, the named residues will be excluded from both of the input files before the areas are calculated.

MATCHUP ALL | NOCOORDS

Default: ALL

In DIFFMODE COMPARE MATCHUP sets the comparision criteria used when doing comparision of XYZIN and XYZIN2:

ALL

(default) Atoms are only included in the comparision compared if atom name, residue name/number, chain id and atomic coordinates are the same between both files.

NOCOORDS

Uses the same criteria as ALL, except that differences in the atomic coordinates between the files are ignored. This makes it suitable for use with different conformations.

Atoms which are not included in the comparision are ignored in the output. MATCHUP is only available for DIFFMODE COMPARE.

PNTDEN <point_density>

Note: High values of <point_density> allow more precise estimates of the accessible surface area, but will take longer to calculate - and if <point_density> is too large then the program may exceed its memory resources and stop. At lower values of <point_density> it is possible that atoms with low surface accessibility may be diagnosed as having no accesible surface area at all.

PROBE <x>

The probe radius must be greater than zero, up to a limit of 25 A. The default radius is 1.4 A.

Auxiliary Keywords

VERBOSE

1. A list of the recognised atom types and their associated radii (see the ATOM keyword),
2. The matrices derived from the SCALE cards of the input file,
3. The symmetry matrices used to generate symmetry-related atoms in SMODE IMOL or DIFFMODE IMOL

OUTPUT

END

INPUT AND OUTPUT FILES

XYZIN

Input coordinates in CCP4 PDB format. Must contain SCALE cards if symmetry-related molecules are required. Must contain CRYST1 card if the OUTPUT option is being used.

XYZIN2

This gives a second set of input coordinates, and is only used in DIFFMODE COMPARE

XYZOUT

Output coordinate file in a pseudo-PDB format, where the B-factor column contains the accessible area calculated for each of the atoms (or area difference if DIFFMODE is anything other than OFF). This is an attempt to reproduce part of the functionality of the old AREAIMOL program. See keyword OUTPUT.

Notes

1. Atoms with zero occupancy in the input files will be ignored in the area calculations; those with finite occupancies less than unity will be included. In either instance a warning message will appear. Also, the program does not recognise 'TER' cards and will skip them, continuing to read in any atoms appearing afterwards.
2. The program always ignores hydrogens which are present in the input file(s). This is because the van der Waals radii used in the area calculations implicitly include the atomic hydrogens.

PRINTER OUTPUT

The program also outputs the contact area for each residue, chain and for the whole molecule. The contact area is defined as the area on the Van der Waals surface of an atom that can be contacted by a sphere of the given probe radius.

For modes NOHOH and ALL the program analyses the atoms which have been assigned accessible area and tries to determine how many isolated areas of surface there are (i.e. areas of surface which are unnconnected to each other on the original molecule). Multiple isolated surfaces could represent any combination of:

1. cavities within a single molecule,
2. cavities formed as a result of intermolecular contacts (in which case the calculated area will be the area of the part of the cavity formed by a single molecule, and not of the whole cavity), and
3. separate molecules or clusters of atoms.

In the case when differences in area are calculated (DIFFMODE other than OFF), an additional analysis is presented of the number of each atom type which have non-zero area differences. This is summarised in a table with the following quantities:

Number

the number of atoms of each type read in from the input file

Area1(Area2)

the total accessible areas for all atoms of that type from the first (second) area calculations

N-diff

the number of that atom type which have non-zero area differences

Area-diff

the total difference in accessible area for all atoms of that type

There is also a breakdown of accessible area differences by residue, chain and for the whole molecule.

Additional output can be obtained by specifying the VERBOSE keyword. This causes the program to print out diagnostic information such as recognised atom types and radii and the symmetry matrices derived from the symmetry cards.

PROGRAM FUNCTION

There were originally four programs to analyse solvent accessible area (AREAIMOL, RESAREA, WATERAREA and DIFFAREA). This version combines the function of the original set of programs into a single run which is controlled by the DIFFMODE keyword:

DIFFMODE OFF

In the most basic mode of operation the program performs a single area calculation, obtaining the solvent accessibility of each atom under consideration. These individual areas are then used to obtain an analysis of the total accessible area for each residue, chain and for the whole molecule.

The MODE keyword can be used to exclude certain types of residue (e.g. waters) from the calculation. The effect of intermolecular contacts (which will reduce the accessible area) can be included using the SMODE keyword (which generates symmetry-related copies of the original molecule by applying the symmetry operations supplied with the SYMMETRY keyword) and the TRANS keyword (which will apply linear combinations of primitive lattice vectors to the symmetry-related molecules to generate further copies). Combining the primitive lattice vectors with spacegroup symmetry will effectively generate the crystal lattice.

This reproduces the function of the old AREAIMOL program followed by either WATERAREA or RESAREA as appropriate.

DIFFMODE IMOL

Two area calculations are performed, one for each set of supplied symmetry operations (see SYMMETRY and TRANS keywords - if only one set of operators is supplied then the second set is assumed to consist of the identity). The difference in accessible area on each atom is then calculated and the overall area differences analysed.

The SMODE keyword has no function under the DIFFMODE IMOL option, and the SYMMETRY keyword can appear twice: each occurance gives the operators for one calculation of accessible area. Other keywords maintain their function and take effect during both calculations.

DIFFMODE WATERS

Only one set of coordinates is input, and two separate area calculations are carried out (the first treating waters as solvent, i.e. equivalent to MODE HOH, and the second treating them as protein, i.e. equivalent to MODE HOHALL). The area differences are then calculated and output.

The results of the calculations can be interpreted as follows:

1. Waters with zero area in the first calculation are completely enclosed by protein.
2. Waters which have non-zero area in the first calculation but zero area in the second are enclosed between protein and/or other waters
3. Waters which have non-zero area in both calculations are not completely enclosed by protein and/or waters and so are on the `outside' of this shell.

The MODE keyword has no function under this option, although the other keywords maintain their function and take effect during both calculations.

DIFFMODE COMPARE

Two input coordinate files are required, and two separate area calculations are carried out, one for each set of coordinates. The same MODE and symmetry operators etc (if relevant) are used in each case, so the resulting area differences will depend only on differences between the contents of the files. Area differences are calculated only for those atoms which are common to both files.

E.g. if one file describes a protein bound to a ligand and the other describes the protein alone, then using this mode will calculate the change in surface area of the protein in the presence of the ligand, or more specifically the area obscured by the ligand.

GENERAL NOTES

The area calculations also depend critically upon various parameters, such as the probe radius (taken to be 1.4 A for most calculations) and the van der Waals's radii chosen for different atoms. Many programs (including AREAIMOL) choose one radius for all carbons, one radius for all nitrogens, one for all oxygens, whereas others (e.g. SURFACE) are able to differentiate between different carbons (aliphatic, aromatic etc.), different nitrogens and so on.

SURFACE assigns the Van der Waal's radius for a given atom according to both the element and also the residue in which it appears, and thus may lead to differences in estimates of the accessible area.

Note that SURFACE calculates both the accessible area and the contact area, but does not include options for accounting for intermolecular contacts.

EXAMPLES

Unix examples script found in $CEXAM/unix/runnable/