A family is defined as a group of one or more amino acids consecutively
located in the sequence. Families are not something very intelligent
or so, it is just a way of giving names to
stretches of amino acids. One can for example give all major secondary structure
elements their own name. Families can at several stages be used as input for options.
It is for example possible to give families a color, or delete all
residues in a family.
Commands that are related to usage of families are easily recognized because
they have the three letter combination FAM in their name.
A cluster is a group of residues that does not need to sit next to each
other in the sequence. In a way clusters are sets of families.
Commands that are related to usage of clusters are easily recognized because
they have the three letter combination CLU in their name.
There are no restrictions to residues in families or
clusters, they dont need to contact each other, they can be mixed protein,
nucleic acid, drugs, ions and water, etc. The only problem is that some
options can not accept every cluster as input. E.g. a protein mutation option
can not accept as input range a family that contains drugs.
You can enter this menu with the commands CLUFAM, CLUSTER or FAMILY.
The general (is menu independent) option CHOOSE pre-selects a cluster.
Every WHAT IF option that accepts clusters if residue input is required will, after
using CHOOSE, use the cluster you created with the CHOOSE command instead of
prompting you for residues. The NEWRNG command disables the CHOOSE option.
WHAT IF's entire memory about families can be initialized withe the INIFAM
command. This command does not do anything with the amino acids that are
in those families, just the information about the groupings will be erased.
The command SHOFAM can be used to get a listing of all presently available
families.
The command SETFAM will cause WHAT IF to prompt you for a residue range and
a family name. The range will under that name be stored as a family.
The command DELFAM will cause WHAT IF to prompt you for a
a family name. This family will be removed from the list of families..
The command INICLU will cause WHAT IF to erase all information about the
grouping of amino acids in clusters from its memory. Nothing is done with
the amino acids themselves.
The command SHOCLU can be use to inspect the contents of a cluster. You will
be prompted for the number of the cluster.
The command SETCLU will cause WHAT IF to prompt you for ranges of residues
(finish input of ranges with a zero as usual), and for a cluster name.
A hydrophobic cluster is a group of amino acids which is generated by
the following set of rules:
1) No amino acid has an accessibility above a certain threshold value
(default = 1.0 Angstrom**2).
2) Every amino acid in the cluster is close to
at least two other amino acids in the cluster; being close is defined as having
at least one pair of atoms within a certain distance from each other (default =
5.0 Angstrom.
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The command HYDCLU will cause WHAT IF to prompt you for a residue and
a residue range. It will
try to generate the largest cluster (see above for definition) in
the range with the first given residue in it.
If WHAT IF prompts you for residues, it always asks you to give:
One residue
One range of residues
Multiple ranges of residues
If you are prompted for one residue, well, that is exactly what you can do:
give one residue.
If you are prompted for one range, you can give ranges as usual, but you can also
type the name of a family. The range of this family will become the input to the
option.
If you are prompted for multiple ranges you can, every time when you
are prompted for a range, give a range as usual, give the name of a family,
or give the name of a cluster. If you give ranges, families, or clusters with
overlapping residues that all residues will be used by the option that
are part in at least one of those ranges, families or clusters.
The following parameters influence the behaviour of at least one of the
cluster or family options:
The LIMBUR parameter in the parameters menu of the ACCESS menu determines
the maximal allowed accessible surface in order for a residue to be called
buried by the HYDCLU option.
The VDWOVR parameter in the parameters menu of the ACCESS menu determines
the maximal allowed distance between the Van der Waals' surfaces of two
atoms in order for to be called a contact in the HYDCLU option. (This is the
same parameter as VDWDST in the WATER parameter menu).
The parameter AA1OR3 in the general parameter menu (you enter that menu
with the SETPAR command) determines if the SHOCLU and SHOFAM commands list
the residues in 1 or 3 letter code.