SYBYL

General Naming Conventions

• Names of atoms and substructures: 7 characters

• Names of sets/features: 31 characters

• Names of molecules: any no. of characters enclosed in double quotes

• Names are case insensitive

• To start with an alphabetic character A-Z
  May contain digits, underscores, apostrophe.

• Wild characters for selecting objects:
  * -> any no. of characters of any type
  @ -> a single character of any type
  

Atom selection

• Atom id
  a single number (which may change !!)
• Atom name
  According to the general rules.
  - Valid examples: CA CA12' C_01
  - Invalid examples: 1C C(1)
  May also contain substructure name:
  - HIS1.CA for Calpha of substructure HIS1
  - His1.* for all atoms of residue HIS1
  - *.ca for all Calpha atoms - ST*.C1 for all C1 atoms of all substructures startting with 'ST'
• Molecular area
  e.g. M1 for all atoms of workarea M1
• Atom type
  '<>' designating chemical element and hybridization: <c.3> <o> <n*>
• Substructure or Set name
  Enclosed in '{}'. Examples: {phenyl} {helix} {his*} {sphere(phe20.ca,10.5)}
• Connected path
  Using the ':'. Examples C1:C10 and 23:48
• Substructure path
  Combination of '{}' and ':'. Examples: {his1:phe10} {1:10}

Bond selection

• Bond id
  a single number (which may change !!)
  list bond *
• Single atom name
  All bonds to that specific atom
• Specific bond
  Using the '=' Examples: C1=C10 His1.CA=His1.CB 3=7
• Bond type
  Example: <2>
• Molecular area
  e.g. M1 for all bonds of workarea M1
• Connected path
  Using the ':'. Examples N1:S10 G2.C3:A7.C3
  Beware of rings !!
• Substructure or Set name
  Examples: {A1} {his1}
• Substructure path
  Combination of '{}' and ':'. Examples: {his1:phe10} {1:10}

Language specifications

Object expressions using logical operators:

• '+' for union
• '&' for intersection
• '-' for difference
• '~' for negation

Sets

• Dynamic sets:
  Membership is evaluated
  Definition using a rule
  Example:
  define dynamic_set subst {sphere(A17.C1,10.5)} active-site "10 A radius around A17"
  and subsequently use this definition by e.g.
  color {active-site} red
• Static sets:
  Membership doesn't change (as long as the structure doesn't change)
  Definition using a rule or a name
• Built-in sets
  Examples: polar, bulky, backbone, acidic

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