Moloc: Molecular Modelling on UNIX Workstations: 6 Perform Set Manipulations [uxx, set name]
Perform Set Manipulations [uxx, set name]
With this tool the user can define up to 32 sets of atoms.
Such sets are used on different occasions (deleting atoms,
coloring substructures, define fixed atoms etc.). Boolean
operations on several sets are possible. Picking with the
left mouse button adds to the current set, picking with the
middle button removes from the current set. The sets are
labelled uxx, where u stands for user and xx is a number
between 0 and 31.
a: atoms
Add or remove single atoms.
e: entries
Add or remove whole entries.
m: monomers
Add or remove monomers, where defined.
s: substituents
Add or remove substituents. The first atom picked will
not be included. The second atom picked must be bonded
to the first and is the first to be counted to the sub
stituent. All atoms connected to the second atom by a
bond path (not leading through the bond to the first
atom) belong to the substituent.
l: loops
Add or remove loops. The first atom picked will not be
included. The second atom picked must be bonded to the
first and is the first to be counted to the loop. The
third atom picked indicates the end of the loop, and is
not considered a member of the loop. All atoms con
nected to the second atom by a bond path (not leading
through the first or third atom) belong to the loop.
f: fragments
All atoms connected to the picked atom or bond belong to
the fragment. This option is identical with the entry
option for a single structure.
d: distance criteria from current set
All atoms which are at a distance smaller than a chosen
threshold from one of the atoms of the current set will
be included in the new set. Only active entries are con
sidered. One has the choice to have all atoms of a mono
mer included in the new set if one of them fulfills the
criterion.
&: and into present set
A list of existing sets will be presented. An atom is
only kept in the current set if it is also a member of
all chosen sets.
|: or into present set
A list of existing sets will be presented. All atoms of
the chosen sets will be added to the current set.
!: not into present set
A list of existing sets will be presented. An atom is
only kept in the current set if it is not a member of
any of the chosen sets.
r: remove sets (no atoms deleted!)
A list of existing sets will be presented. All the cho
sen sets will be removed. The corresponding space is
available to define new sets.
c: change current set
Any of the previously defined sets can be chosen as the
current one. If the current set was not empty, it is
kept. It is also possible to start with a new set here.
v: view other sets
All currently defined sets can be chosen to be dis
played here.
j: write disk-file of current set
Of the current set a disk file is written. Supported
formats are .jkl and .pdb type files.
n: look at a single entry
Choosing this option puts the focus on a single entry.
Some additional options of generic and literal atom
specification are then possible.
n: look at a single entry
With this option you focus on a single entry. You have
to the above option (except option n) the following
additional ones:
t: atoms by type
Type the chemical symbol of the element. This is not
case sensitive.
n: atoms by name
Type the name of the atoms. This is case sensitive.
+,-: add, remove
toggle between add and remove. The atoms defined by
'atoms by type\q (t), \qatoms by name\q (n) or \qpolymer\q
(p) are added or removed resp.
p: polymer
Special polymer function like sequence number, backbone etc.
(see next section)
)