2.3 The Command-Line Options

Most of these options can be combined together, eg -IxLo, but those options
that expect an argument must be solitary (eg -a 60.0) or at the end of a
"set" (eg -ILoxa 60.0).  The most oft-used command-line options are '-O' (to
give a PDB format file that includes all polar hydrogens) and '-Q' (to
analyse the preferred orientations of Asn, Gln and His side-chains).

-a      The next argument is the minimum angle.  This option sets the
minimum D-H-A, H-A-AA and D-A-AA angles (Default 90.0 degrees).  See below
for the definition of these angles.

-A	The next three arguments are the minimum D-H-A, H-A-AA and D-A-AA
angles, respectively.

-b      The next argument is the maximum angle with the perpendicular for
amino-aromatic hydrogen bonds (Default 20.0 degrees).  This only matters if
the "R" option has been used to switch aromatic hydrogen bonds on.

-B      The next two arguments are the maximum H-A-Perpendicular and
D-A-Perpendicular, respectively, where "Perpendicular" is the line
perpendicular to the plane of an aromatic acceptor running throught the
putative acceptor.

-c/C	In the output, change CYS SG to CSS SG or CYH SG, the former
indicating that the sulphur is involved in a disulphide bridge.  (The default
is to refer to all cysteines and cystines as CYS).

-d/D	The next argument is the maximum D-A distance, in Angstroms
(Default 3.9 Angstroms).

-e/E    This is used in the form "-e/E atomname number".  The number of
hydrogen bonds that atom "atomname" is theoretically able to donate ("E")
or accept ("e") is set to "number".  Although it rarely makes practical
difference in this release of HBPLUS whether an atom is declared to be able
to accept 1, 2 or 3 hydrogen bonds, including the number is still
obligatory.  It DOES make a difference to donors, as it is also the number
of hydrogens to add to the *.h structure output with the "o" option.  The
setting "-1" is used for aromatic acceptors.  The format of "atomname" is
the same as in the output files and must be exactly seven characters long.
Preceding and trailing spaces must be included.  For example "-e 'MET SG '
0" redeclares the methionine sulphur as incapable of hydrogen bonding, and
"-e 'PRO N ' 1" declares the proline nitrogen as a hydrogen bond acceptor.
See section 2.6.

-f	The next argument names a file of command-line options.  The syntax
of this file is rather like the UNIX shell - "#" introduces comments and
the three quote types """, "`" and "'" are used, but escape characters are not
recognised.

-h/H	The next argument is the maximum H-A distance, in Angstroms
(Default 2.5 Angstroms).

-K	Use Kabsch-Sander positions for the hydrogens (ie with the NH bond
parralel to the preceding CO bond) rather than the Pauling position
(bisecting CA-N-C).

-k	Use the Pauling position (default).

-M	The next two arguments are a residue name and a list of atoms to be
added to that residue's list of included atoms.  See section 2.6

-N 	Generate a list of neighbours, rather than hydrogen bonds.
Covalently bonded and nearly-bonded contacts are excluded, but all other
contacts within the maximum D-A distance are listed.  The output file
suffix changes from .hb2 to .nb2 [or, if used with the -L options, from
.hhb to .nnb].

-n      Disables "neighbours" option.  Generate the list of hydrogen bonds.
As you may have gathered, this is the default.

-o/O	Output a *.h file of atomic co-ordinates that include hydrogens.
The format is an abbreviation of the Brookhaven data file.  (Default is not
to do this.)

-P	Output a list of all donors and acceptors.  Aromatic acceptors can
accept "-1 H-Bonds".

-q	Input a .asa file output by Simon Hubbard's program ACCESS (1992,4).
HBPLUS looks for a file in the current directory that has the same name as
the brookhaven file, but the .asa suffix. [Version 3.0 onwards]

-Q 	Input a .asa file from ACCESS, and investigate the H-bonding 
patterns of ASN, GLN and HIS side-chains, producing a listing of H-bonds by
side-chain and atom accessibilities, and classifying the conformation in
the PDB file relative to the alternative as "Highly Suspect", "Slightly
Suspect", "Indifferent", "Slightly Optimal" or "Highly Optimal", depending
on which conformation further satisfied hydrogen bonding potential.  This
automatically triggers the '-X' option. [Version 3.0 onwards]

-R      Allow atoms in the aromatic rings of Tyr, Trp and Phe to accept
amino-aromatic hydrogen bonds.

-r      Disables amino-aromatic hydrogen bonds (the default).

-s/S	The next argument is the cutoff distance for assigning a disulphide
bridge.  (Default 3.0 Angstroms)

-T	The next argument is a residue and the subsequent argument is a
list of covalent bonds formed within that residue.  See section 2.6.

-u      The next argument is a residue to be added to the HBPLUS residue
list.  See section 2.6

-U	The next argument is a residue that is predefined as having all the
atoms, covalent bonds and hydrogen bond donors and acceptors of the residue
named in the subsequent argument.  See section 2.6

-v/V    The next argument is the number of covalent bonds that count as
nearly bonded.  Contacts that are "nearly bonded" do not count as hydrogen
bonded.  The default is two.

-x      Exchange the side-chains of Histidine, Glutamine and Asparagnine.
These side-chains are difficult to resolve crystallographically with
certainty, which is why there is the option of adding potential hydrogen
bonds that would be formed if HIS CD2 was actually ND1, HIS CE1 was NE2 and
the nitrogens and oxygens of the ASN / GLN amide groups were actually the
other way round.  (Default is not to do this.)

-X      As -x, but only hydrogen bonds formed by HIS, GLN and ASN side-chains
are included in the hydrogen bond list.  This is a time-saving option when
your purpose is to investigate the hydrogen bonding of HIS, GLN and ASN
side-chains.

[ The following options relate to the way the program is used in its "home"
laboratory, and are only really included for completeness ]

-i	Do not attempt to load an sst file and input the secondary
structure of the protein (default).

-I      Attempt to load an sst file and input the secondary structure.  The
program looks for a file with the filename "p????.sst" where ???? is the
 four-letter brookhaven code taken from the header line.

-l	Output in *.hb2 format (the default).

-L      Output in long *.hhb format, which is an extended version of the
HBOND table in IDITIS (Oxford Molecular 1993), and includes the secondary
structural information taken from an sst file.