Under Construction !
General Remarks
number
leaving
purpose
current
Direct Specification
Various structural elements can be added to (left-hand mouse button) or removed
from (middle mouse button) the current set by picking appropriate elements:
- a single atoms by picking them
- e whole entries by picking an atom or bond
- m whole monomers of a polymer by picking an atom or bond
- s substituents by picking the two atoms of the bond
leading to the substituent. Pick the atom on the substituent side last!
- l loops. Three atoms must be picked. The first and second
specify a bond leading to the loop (see option s). The third one terminates
the loop and will not be included.
Option s and l can be understood in terms of a path that is initiated by the
specified bond and continues in all possible directions, with the constraint(s)
that reusing the initial bond is prohibited as well as visiting the end-loop
atom.
- f whole fragments by picking an atom or bond. For
single-fragment entries this is equivalent to option e.
Distance Criteria
Boolean Manipulations
When choosing a boolean option a list of current sets will be presented. All
atoms occurring in one of the specified sets will be used as a partner set for
the current one in one of the following operations:
- & keep only atoms that occur in both sets.
- | keep all atoms that occur any of the two sets.
- ! keep only atoms of the current set that do not occur
in the partner set.
Set Handling
The following set-handling options are provided:
- r remove sets (no atoms are deleted!)
- c change current set. Any of the existing sets can be
made the current one. In addition, a new (empty set) can be specified.
- v Existing sets can be viewed one by one.
- j A disk file is written which contains all atoms of the
current set. Provided formats are .jkl, and .pdb
(->file formats).
Working with a Single Entry
If a single entry is specified (option n, pick it) additional
specification modes become meaningful, namely specification by atom name
(option n) or by atom type (option t).
For these two options the toggle (+/-) indicates whether the specified atoms
should be added to or removed from the set.
If the entry is a polymer, an additional option p leads into
a new menu with the following options:
- n:
Polymer-Specific Options