Specifying Atom Subsets
Keywords: ProFit

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Specifying Atom Subsets

The `ATOMS` command is used to specify a subset of atoms to be used in the calculations. It has the syntax:

       ATOMS atm[,atm]...

i.e. you specify the `ATOMS` keyword followed by one or more atom names separated by commas. A `*` may be used to specify all atoms and a `~` or `^` may be placed at the beginning of the specification to inverse the selection. For example, to fit only C atoms:

       ATOMS CA

to fit N, C, C and O atoms:

       ATOMS N,CA,C,O

to fit sidechains only (i.e. everything except N, C, C and O atoms):

       ATOMS ^N,CA,C,O

to return to fitting all atoms:

       ATOMS *

The PDB atom name field is 4 characters wide followed by a space. The first two characters are the right-justified element type, so for normal protein and DNA atoms consist of a space followed by a N, C, O, S or P. Thus the atom name field for a C contains ` CA '. HETATMs such as calcium will contain the two characters CA in the first two fields. i.e. `CA '. When you specify an atom type it is matched against the atom name field from the second character onwards, unless you preceed it with a `<`. Thus to match a C you use `CA`, but to match Calcium, you use `<CA`. For example, as stated above, to match C atoms:

       ATOMS CA

while to match calcium atoms

       ATOMS <CA

and to match both C and calcium:

       ATOMS <CA,CA

Wildcards are also allowed. A `%` or a `?` may be used to match a single letter at any point in the specification while a `*` may be used to match all remaining characters (thus `C*` is allowed, but `*G` is not). These special characters may be escaped by preceding them with a `\`. For example to fit all carbons:

       ATOMS C*

or to match all atoms at the position:

       ATOMS ?G*

and to match the `C4*` atoms in DNA:

       ATOMS C4\*

If atom names contain spaces (e.g. in heme groups) the whole atom specification must be enclosed in double inverted commas:

       ATOMS "N A,N B,N C"

Next: Specifying Zones Up: ProFit V2.2 Previous: Fitting Structures