Esempio n. 1
0
def align_1kx5():
    '''
    align the 1kx5 to the dimer then save pdbs for psfgen
    '''
    mono_file = '1KX5tailfold_fx_CG.pdb'
    # goal_file = 'new_c11_tetramer.pdb'
    goal_file = 'c11_folded_tails.pdb'

    in_vars = inputs()
    in_vars.goal = goal_file
    in_vars.ref = in_vars.move = mono_file
    in_vars.path = './'
    in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))'

    # NCP 1
    in_vars.out = '4mer_ncp1/1KX5_4mer_ncp1.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 22) and (resid[i] < 170))'
    align.align(in_vars)

    # NCP 2
    in_vars.out = '4mer_ncp2/1KX5_4mer_ncp2.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 189) and (resid[i] < 337))'
    align.align(in_vars)

    # NCP 3
    in_vars.out = '4mer_ncp3/1KX5_4mer_ncp3.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 356) and (resid[i] < 504))'
    align.align(in_vars)

    # NCP 4
    in_vars.out = '4mer_ncp4/1KX5_4mer_ncp4.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 523) and (resid[i] < 671))'
    align.align(in_vars)
Esempio n. 2
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def align_1kx5():
    '''
    align the 1kx5 to the dimer then save pdbs for psfgen
    '''
    mono_file = '1KX5tailfold_fx_CG.pdb'
    # goal_file = 'new_c11_tetramer.pdb'
    goal_file = 'c11_folded_tails.pdb'

    in_vars = inputs()
    in_vars.goal = goal_file
    in_vars.ref = in_vars.move = mono_file
    in_vars.path = './'
    in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))'

    # NCP 1
    in_vars.out = '4mer_ncp1/1KX5_4mer_ncp1.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 22) and (resid[i] < 170))'
    align.align(in_vars)

    # NCP 2
    in_vars.out = '4mer_ncp2/1KX5_4mer_ncp2.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 189) and (resid[i] < 337))'
    align.align(in_vars)

    # NCP 3
    in_vars.out = '4mer_ncp3/1KX5_4mer_ncp3.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 356) and (resid[i] < 504))'
    align.align(in_vars)

    # NCP 4
    in_vars.out = '4mer_ncp4/1KX5_4mer_ncp4.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 523) and (resid[i] < 671))'
    align.align(in_vars)
Esempio n. 3
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def main():
    ''' 
    this did not work well, there histones to not match well 
    in the NCP so there was overlap btwn the aligned versions
    '''
    in_vars = inputs()

    goals = [
        'histone_A0.pdb', 'histone_B0.pdb', 'histone_C0.pdb', 'histone_D0.pdb',
        'histone_E0.pdb', 'histone_F0.pdb', 'histone_G0.pdb', 'histone_H0.pdb',
        'histone_A1.pdb', 'histone_B1.pdb', 'histone_C1.pdb', 'histone_D1.pdb',
        'histone_E1.pdb', 'histone_F1.pdb', 'histone_G1.pdb', 'histone_H1.pdb'
    ]
    move = [
        '1KX5tailfold_167bp_chain_A1.pdb', '1KX5tailfold_167bp_chain_B1.pdb',
        '1KX5tailfold_167bp_chain_C1_trun.pdb',
        '1KX5tailfold_167bp_chain_D1.pdb', '1KX5tailfold_167bp_chain_A1.pdb',
        '1KX5tailfold_167bp_chain_F1.pdb',
        '1KX5tailfold_167bp_chain_G1_trun.pdb',
        '1KX5tailfold_167bp_chain_H1.pdb'
    ]
    out = [
        '1H3.pdb', '1H4.pdb', '1H2A.pdb', '1H2B.pdb', '2H3.pdb', '2H4.pdb',
        '2H2A.pdb', '2H2B.pdb', '3H3.pdb', '3H4.pdb', '3H2A.pdb', '3H2B.pdb',
        '4H3.pdb', '4H4.pdb', '4H2A.pdb', '4H2B.pdb'
    ]
    move_seg = ['A', 'B', 'C', 'D', 'A', 'F', 'G', 'H']
    goal_seg = [
        'A0', 'B0', 'C0', 'D0', 'E0', 'F0', 'G0', 'H0', 'A1', 'B1', 'C1', 'D1',
        'E1', 'F1', 'G1', 'H1'
    ]
    in_vars.move_seg_or_ch = 'segname'
    in_vars.goal_seg_or_ch = 'segname'
    in_vars.path = './'
    match_res_min = [50, 20, 01, 50]
    match_res_max = [70, 40, 50, 124]

    for i in xrange(len(goals)):
        in_vars.goal = goals[i]
        in_vars.move = in_vars.ref = move[i % 8]
        in_vars.out = out[i]
        in_vars.move_seg_chain = move_seg[i % 8]
        in_vars.goal_seg_chain = goal_seg[i]
        in_vars.min = match_res_min[i % 4]
        in_vars.max = match_res_max[i % 4]

    align.align(in_vars)
def align_1kx5():
    '''
    align the 1kx5 to the dimer then save pdbs for psfgen
    '''
    mono_file = '1KX5tailfold_fx_CG.pdb'
    goal_file = 'gH5_NCP.pdb'

    in_vars = inputs()
    in_vars.goal = goal_file
    in_vars.ref = in_vars.move = mono_file
    in_vars.path = './'
    in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))'

    # NCP 1
    in_vars.out = '4mer_ncp1/1KX5_4mer_ncp1.pdb'
    in_vars.goal_filter = '((segname[i] == "I") and (name[i] == "C1\'") and (resid[i] >= 11) and (resid[i] <= 157))'
    align.align(in_vars)
Esempio n. 5
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def align_1kx5():
    '''
    align the 1kx5 to the dimer then save pdbs for psfgen
    '''
    mono_file = '1KX5tailfold_fx_CG.pdb'
    goal_file = 'gH5_NCP.pdb'

    in_vars = inputs()
    in_vars.goal = goal_file
    in_vars.ref = in_vars.move = mono_file
    in_vars.path = './'
    in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))'

    # NCP 1
    in_vars.out = '4mer_ncp1/1KX5_4mer_ncp1.pdb'
    in_vars.goal_filter = '((segname[i] == "I") and (name[i] == "C1\'") and (resid[i] >= 11) and (resid[i] <= 157))'
    align.align(in_vars)
Esempio n. 6
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def mv_A_to_E():
    '''
    this worked well to move A to E (no apparent overlap)
    '''
    in_vars = inputs()
    in_vars.goal = '1KX5tailfold_167bp_chain_E1.pdb'
    in_vars.ref = '1KX5tailfold_167bp_chain_A1.pdb'
    in_vars.move = '1KX5tailfold_167bp_chain_A1.pdb'
    in_vars.out = '1KX5tailfold_A2E_2.pdb'
    in_vars.move_seg_chain = 'A'
    in_vars.goal_seg_chain = 'E'
    in_vars.path = './'
    in_vars.move_seg_or_ch = 'segname'
    in_vars.goal_seg_or_ch = 'segname'
    in_vars.min = 38
    in_vars.max = 50

    align.align(in_vars)
def mv_A_to_E():
    '''
    this worked well to move A to E (no apparent overlap)
    '''
    in_vars = inputs()
    in_vars.goal = '1KX5tailfold_167bp_chain_E1.pdb'
    in_vars.ref = '1KX5tailfold_167bp_chain_A1.pdb'
    in_vars.move = '1KX5tailfold_167bp_chain_A1.pdb'
    in_vars.out = '1KX5tailfold_A2E_2.pdb'
    in_vars.move_seg_chain = 'A'
    in_vars.goal_seg_chain = 'E'
    in_vars.path = './'
    in_vars.move_seg_or_ch = 'segname'
    in_vars.goal_seg_or_ch = 'segname'
    in_vars.min = 38
    in_vars.max = 50

    align.align(in_vars)
Esempio n. 8
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def main():
    ''' 
    this did not work well, there histones to not match well 
    in the NCP so there was overlap btwn the aligned versions
    '''
    in_vars = inputs()

    goals = ['histone_A0.pdb', 'histone_B0.pdb', 'histone_C0.pdb', 'histone_D0.pdb',
             'histone_E0.pdb', 'histone_F0.pdb', 'histone_G0.pdb', 'histone_H0.pdb',
             'histone_A1.pdb', 'histone_B1.pdb', 'histone_C1.pdb', 'histone_D1.pdb',
             'histone_E1.pdb', 'histone_F1.pdb', 'histone_G1.pdb', 'histone_H1.pdb']
    move = ['1KX5tailfold_167bp_chain_A1.pdb', '1KX5tailfold_167bp_chain_B1.pdb',
            '1KX5tailfold_167bp_chain_C1_trun.pdb', '1KX5tailfold_167bp_chain_D1.pdb',
            '1KX5tailfold_167bp_chain_A1.pdb', '1KX5tailfold_167bp_chain_F1.pdb',
            '1KX5tailfold_167bp_chain_G1_trun.pdb', '1KX5tailfold_167bp_chain_H1.pdb']
    out = ['1H3.pdb', '1H4.pdb', '1H2A.pdb', '1H2B.pdb',
           '2H3.pdb', '2H4.pdb', '2H2A.pdb', '2H2B.pdb',
           '3H3.pdb', '3H4.pdb', '3H2A.pdb', '3H2B.pdb',
           '4H3.pdb', '4H4.pdb', '4H2A.pdb', '4H2B.pdb']
    move_seg = ['A', 'B', 'C', 'D', 'A', 'F', 'G', 'H']
    goal_seg = ['A0', 'B0', 'C0', 'D0',
                'E0', 'F0', 'G0', 'H0',
                'A1', 'B1', 'C1', 'D1',
                'E1', 'F1', 'G1', 'H1']
    in_vars.move_seg_or_ch = 'segname'
    in_vars.goal_seg_or_ch = 'segname'
    in_vars.path = './'
    match_res_min = [50, 20, 01, 50]
    match_res_max = [70, 40, 50, 124]

    for i in xrange(len(goals)):
        in_vars.goal = goals[i]
        in_vars.move = in_vars.ref = move[i % 8]
        in_vars.out = out[i]
        in_vars.move_seg_chain = move_seg[i % 8]
        in_vars.goal_seg_chain = goal_seg[i]
        in_vars.min = match_res_min[i % 4]
        in_vars.max = match_res_max[i % 4]

    align.align(in_vars)
Esempio n. 9
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def align_1kx5():
    '''
    align the 1kx5 to the dimer then save pdbs for psfgen
    '''
    mono_file = '1KX5tailfold_fxd.pdb'
    dimer_file = '../150205dimer.pdb'

    in_vars = inputs()
    in_vars.goal = dimer_file
    in_vars.ref = in_vars.move = mono_file
    in_vars.path = './'
    in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))'

    # NCP 1
    in_vars.out = '1KX5tailfold_dimer_ncp1.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 14) and (resid[i] < 162))'
    align.align(in_vars)

    # NCP 2
    in_vars.out = '1KX5tailfold_dimer_ncp2.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 181) and (resid[i] < 329))'
    align.align(in_vars)
Esempio n. 10
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def align_1kx5():
    '''
    align the 1kx5 to the dimer then save pdbs for psfgen
    '''
    mono_file = '1KX5tailfold_fxd.pdb'
    dimer_file = '../150205dimer.pdb'

    in_vars = inputs()
    in_vars.goal = dimer_file
    in_vars.ref = in_vars.move = mono_file
    in_vars.path = './'
    in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))'

    # NCP 1
    in_vars.out = '1KX5tailfold_dimer_ncp1.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 14) and (resid[i] < 162))'
    align.align(in_vars)

    # NCP 2
    in_vars.out = '1KX5tailfold_dimer_ncp2.pdb'
    in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 181) and (resid[i] < 329))'
    align.align(in_vars)
Esempio n. 11
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                 '4x167/run7/monte_carlo/4x167_5d_20k.dcd']

start_dir = os.getcwd()

all_dcds = ['4x167/run0/monte_carlo/test.dcd']

align_basis = ('((name[i] == "CA") and (segname[i] == "3H2A") and '
               '(resid[i] > 105) and (resid[i] < 115))')

inputs = align.inputs()


inputs.path = ''
inputs.goal_filter = align_basis
inputs.move_filter = align_basis

dimer = '/home/schowell/myData/sassieRuns/2x167_k010_s1_min.pdb'
trimer = '/home/schowell/myData/sassieRuns/3x167_min.pdb'
tetramer = '/home/schowell/myData/sassieRuns/c11_min.pdb'

inputs.goal = inputs.ref = dimer
for dcd in dimer_dcds:
    print 'aligning %s' % dcd
    inputs.move = os.path.join(start_dir, dcd)
    inputs.out = inputs.move.replace('.dcd', '_al.dcd')
    align.align(inputs)
    os.system('mv %s %s' % (inputs.out, inputs.move))


print '\m/ >.< \m/'
Esempio n. 12
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    '4x167/run6/monte_carlo/4x167_5d_20k.dcd',
    '4x167/run7/monte_carlo/4x167_5d_20k.dcd'
]

start_dir = os.getcwd()

all_dcds = ['4x167/run0/monte_carlo/test.dcd']

align_basis = ('((name[i] == "CA") and (segname[i] == "3H2A") and '
               '(resid[i] > 105) and (resid[i] < 115))')

inputs = align.inputs()

inputs.path = ''
inputs.goal_filter = align_basis
inputs.move_filter = align_basis

dimer = '/home/schowell/myData/sassieRuns/2x167_k010_s1_min.pdb'
trimer = '/home/schowell/myData/sassieRuns/3x167_min.pdb'
tetramer = '/home/schowell/myData/sassieRuns/c11_min.pdb'

inputs.goal = inputs.ref = dimer
for dcd in dimer_dcds:
    print 'aligning %s' % dcd
    inputs.move = os.path.join(start_dir, dcd)
    inputs.out = inputs.move.replace('.dcd', '_al.dcd')
    align.align(inputs)
    os.system('mv %s %s' % (inputs.out, inputs.move))

print '\m/ >.< \m/'