symmetry problems

[Gail Bartlett <>]

Dear Modellers,

Help!  I am trying to generate a homology model of a dimer using a known
structure which is tetrameric.  I want to impose tetrameric symmetry on
the model, but cannot do this on the whole chain as the two halves which
correspond to each tetramer in the known structure are different in
length.  I have selected four segments, two from each dimer,
which should be symmetrical, and have set them to be symmetrical using the
'defsym' subroutine.  This works fine, but if I try to repeat this using
another set of four segments which should also be identical, the program
seems to lock up.  The top file that I used is below:

# Symmetry 
# Define the segments (chains in this case) to be identical: 
DEFINE_STRING VARIABLES = SEG1 SEG2 SEG3 SEG4 
CALL ROUTINE = 'defsym', SEG1 = '5:' '29:', SEG2 = '157:' '181:', SEG3 = 
'249:' '273:', SEG4 = '401:' '425:'

DEFINE_STRING VARIABLES = SEG5 SEG6 SEG7 SEG8
CALL ROUTINE = 'defsym', SEG5 = '79:' '91:', SEG6 = '185:' '197:', SEG7 =
'323:' '335:', SEG8 = '429:' '441:'

SET DYNAMIC_SPHERE = off 
ENERGY 
WRITE_MODEL FILE = 'define_symmetry-1.atm' OPTIMIZE MAX_ITERATIONS = 300
WRITE_MODEL FILE = 'define_symmetry-2.atm' 
ENERGY

SET DYNAMIC_SPHERE = on 
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' 
RANDOMIZE_XYZ DEVIATION = 3.0
SET MAX_ITERATIONS = 300, 
MD_RETURN = 'FINAL' OPTIMIZE OPTIMIZATION_METHOD = 1 # Conjugate gradients
OPTIMIZE OPTIMIZATION_METHOD = 3 # Molecular dynamics 
OPTIMIZE OPTIMIZATION_METHOD = 1 # Conjugate gradients 
WRITE_MODEL FILE = 'define_symmetry-3.atm'
ENERGY

SUBROUTINE ROUTINE = 'defsym' 
SET ATOM_TYPES = 'MNCH' 
SET RES_TYPES = 'ALL' 
SET SELECTION_STATUS = 'INITIALIZE' 
SET SELECTION_SEARCH = 'SEGMENT'

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG1
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG2
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG1
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG3
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG1
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG4
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG2
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG3
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG2
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG4
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG3
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG4
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG5
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG6
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG5
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG7
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG5
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG8
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG6
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG7
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG6
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG8
  DEFINE_SYMMETRY ADD_SYMMETRY = on off

  SET SYMMETRY_WEIGHT = 1.0
  PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = SEG7
  PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = SEG8
  DEFINE_SYMMETRY ADD_SYMMETRY = on off
  
RETURN
END_SUBROUTINE

Many thanks for any help you can give.

Gail Bartlett