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Next: Specifying Zones Up: ProFit Version 3.1 Previous: Fitting Structures

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$\alpha$ atoms:

   ATOMS CA

to fit N, C$\alpha$, C and O atoms:

   ATOMS N,CA,C,O

to fit sidechains only (i.e. everything except N, C$\alpha$, 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$\alpha$ 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$\alpha$ you use CA, but to match Calcium, you use <CA. For example, as stated above, to match C$\alpha$ atoms:

   ATOMS CA

while to match calcium atoms

   ATOMS <CA

and to match both C$\alpha$ 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 $\gamma$ 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 up previous
Next: Specifying Zones Up: ProFit Version 3.1 Previous: Fitting Structures
Andrew Martin 2010-09-28