MODEL : Build molecule from map

limits sets search parameters for Fourier peaks
conect defines the connectivity of expected atomic sites

MODEL Option Code Arg   Def
  extend input site list sext   extend symmetry sites [a]  
    nose   no symmetry extension \(^{1} \)  
  use atom sites atom   include atom sites on pekbdf  
    noat   exclude atom sites on pekbdf  
  subcluster search conn   use connectivity priority  
    none   no angle limits applied  
    mean   use mean distances and angles  

[a] If the number of molecules per cell is less than the number of symmetry equivalent positions, the input sites will automatically be expanded to include symmetrically equivalent sites (i.e. sext ), otherwise nose is the default. The user may override these defaults with this option.

limits [a] 1 bond connections permitted for each atom (max 12) 4
  2 min bond radius for peak site (in Ĺ) 0.5
  3 max bond radius for peak site (in Ĺ) 1
  4 min angle allowed in subcluster (in degrees) [b] 85
  5 max angle allowed in subcluster (in degrees) [b] 145
  6 total number of sites (atom and peak) to be entered all
  7 threshold for contact distances to be listed 2.4
  8 increment to atom radii on the bdf 0.1
  9 maximum number of interpretations printed per cluster 3
  10 number of projections to be plotted for each atom cluster 1 for planar clusters,
      2for globular clusters

[a] WARNING: The ability of MODEL to correctly connect peak (not atom) sites is very dependent on the values in fields 1-5 being appropriate for the structure under study.

[b] See also subcluster search mode on the MODEL line.

conect 1- numeric group numbers or atom labels [a] 1

[a] Numeric fields specify the group number of the atom sites that follow. They are used if several atom fragments or molecules are expected in an asymmetric unit.

Atom labels specify the atoms connected in the group. Connected sites are entered as sequence of atom labels.

(i) an atom label is delimited by a blank

(ii) a sequence is delimited by a semicolon (;) or new conect line

(iii) the central atom is the first label in the sequence

(iv) redundant connections need not be entered

 

          C1     C7
            \  /    \
             C6      C2
             |        |
             C5      C3
               \    /
                 C4

The connections of the preceding fragment would be entered as:

conect C2 C7; C2 C3; C3 C4; C4 C5; C5 C6; C6 C1

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