PATSEE : Search for molecular fragment

FRAG definition of molecular fragment
site atom sites in molecular fragment
zmatrix geometry description matrix
rotate rotational search parameters
transl translational search parameters
triple triple relationship parameters
shift shift coordinates of following atom sites
spin rotate coordinates of following atom sites about Cartesian axes
twist twist following atom sites about connected atom site

PATSEE Option Code Arg   Def
  do not list bond distances and angles of fragments ngeom      

FRAG 1 Use cartesian coordinates on site lines. cart    
    or      
  1-3 cell lengths in Ĺ a, b, c [a]      
  4-6 cell angles in degrees \(\alpha \), \(\beta \), \(\gamma \) [a]      
    or      
  1- labels of atoms to be extracted from lratom: of the input bdf      
    or      
  1 five membered ring pent    
    benzene planar conformation benz    
    benzene boat conformation boat    
    benzene chair conformation chair    

[a] These are applied to the fractional coordinates of the atom sites that follow and must be entered if the cell differs from that on the bdf.

site 1 atom label  
  2-4 coordinates [a]x, y, z  
  5 relative site weight in search ( max 1, min 0 ) 1

[a] Assumed fractional unless the preceding frag line contains the Cartesian code.

zmatrix 1 n1 sequence number  
  2 atom label  
  3 n2 sequence number  
  4 distance to atom n1  
  5 n3 sequence number  
  6 n3-n2-n1 angle  
  5 n4 sequence number  
  6 n1-n2-n3 n2-n3-n4 torsion angle  

rotate Option Code Arg   Def
  number of rotations applied ntry n   auto
  number of solutions saved nsol s   5
  intra-mol. vector angle resolution vres a   10°
  intra-mol. vector d min/max vlim q p q   2. 6.A
  intra-mol. vectors for Rfom (ratio) vfom f   0.5
  intra-mol. vectors for pretest (ratio) vtes r   0.1
  Rfom acceptance threshold fomt t   0.4
  number of refinement searches nref m   1000
  random rotation start value nran r   5431
  rotation start positions about a b c seta a b c   0° 0 ° 0 °
  rotation range about a b c setr a b c   auto
  list all intra-molecular vectors vlis     no
  signal mirror in fragment mirr     no

transl Option Code Arg   Def
  number of translations applied ntry n   auto
  number of solutions saved nsol s   5
  inter-mol. vector d minimum vmin d   3.4 A
  inter-mol. vector shift resolution vres q   0.25 A
  Tfom acceptance threshold fomt t   0.3
  t3sum acceptance threshold tprt f   0.3
  translation origin as x/a y/b z/c [a] sets x y z   0 0 0
  translation range as x/a y/b z/c [a] setr x y z   auto
  list triplets used in t3sum tlis     no
  exclude use of t3sum refinement nots     include
  random translation start value nran r   5431

[a] Six values may be entered; three for the rotation/translation fragment and optionally three for the translation-only fragment.

triple Option Code Arg   Def
  minimum E value used emin e   auto
  minimum A of any triple amin a   auto
  max number of E's used nume n   100
  max number of triples used numt m   100

shift [a] 1-9 rotation matrix elements \(r_{11}\), \(r_{21}\), \(r_{31}\), …, \(r_{33}\)  
  10-12 translation vector \(t_{1}\), \(t_{2}\), \(t_{3}\)  

[a] The shift transformation matrix is applied to all atom sites in the next input fragment.

spin [a] 1-3 rotation angles (in degrees) about the Cartesian axes x, y, z  

[a] A positive value is an anticlockwise rotation as the axis comes towards you. The spin angles are applied to all atom sites in the next input fragment.

twist Option Code Arg   Def
  minimum torsion angle (deg.) tmin a   0
  maximum torsion angle (deg.) tmax b   355
  increment torsion angle (deg.) tinc c   5
  torsion angle test method test i   1


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