ProFit: Warning concerning HETATMs
These changes were implemented in ProFit V2.2. V2.4-V2.5.1 fixed some related bugs which affected multiple-occupancy atoms that were introduced by the changes made for V2.2 If you never used a version of ProFit older than this, then you won't be affected. Similarly, if you never worry about HETATMs, you won't be affected. Otherwise read on!
Following a problem with atom naming in ProFit, some changes have been made with the way atoms are specified.
Atom naming in the PDB
PDB files have a 4-character naming of atoms in columns 13-16 of the PDB records. The first two characters are the element chemical symbol - right justified. The next column is a remoteness indicator (an alphabetic representation of the Greek letter - A=alpha, B=beta, etc.). The final column is a numeric branch designator. In the case of hydrogens where two branch indicators are often needed, the first one appears in column 4 in the normal way and the second one appears in the column 1 (e.g. "1HH1").
Thus, for standard ATOM records, a C-alpha is represented as " CA ", while the HETATM, calcium, is represented as "CA "
What ProFit used to do...
For historic reasons (largely the fact that I used GROMOS a lot in the past), my PDB reader/writer massaged the atom names always to occupy columns 14-17. Column 17 is normally empty in standard PDB files. Thus "1HH1 " became " HH11". Similarly a calcium "CA " became " CA " and is differentiated from a C-alpha by the fact that it is a HETATM instead of an ATOM.
Unfortunately when making an atom selection using the ATOM command in ProFit, there was no way to distinguish between a C-alpha and a Calcium!
Thus 'ATOMS CA' would match both C-alpha and Calcium while 'ATOMS C*' would match all atom types beginning with a C, i.e. it would include Carbon, Calcium and Cobolt.
What ProFit does now...
The code has now been changed such that atom names are no longer massaged when written out by ProFit - what is read in will also be written out.
You can now differentiate between C-alpha and Calcium as follows. The ATOMS command matches against the atom name from the second column of the name, so the command: ATOMS CA refers to C-alpha, i.e. the atom name ' CA '. Similary, C* refer only to carbons.
In order to specify an atom name beginning in the first column one now prefixes the atom type with a < symbol. Thus '<CA' would be used to refer to a Calcium and '<C*' would include Calcium and Cobolt, but not to a C-alpha.