URL:
<http://gna.org/bugs/?12573>
Summary: FAIL: Constrained BFGS opt, backtracking line
search {S2=0.970, te=2048 Rex=0.149}
Project: relax
Submitted by: jhowarth
Submitted on: Thursday 11/06/2008 at 01:52
Category: relax's source code
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: 1.3.2
Operating System: Mac OS X
_______________________________________________________
Details:
On powerpc-apple-darwin9, the following testsuite failure occurs with the
fink relax-py25 package...
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> sequence.read(file='Ap4Aase.seq',
dir='/sw/lib/relax-py25/test_suite/shared_data', mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None,
sep=None)
Opening the file '/sw/lib/relax-py25/test_suite/shared_data/Ap4Aase.seq' for
reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 PRO None None
None 3 LEU None None
None 4 GLY None None
None 5 SER None None
None 6 MET None None
None 7 ASP None None
None 8 SER None None
None 9 PRO None None
None 10 PRO None None
None 11 GLU None None
None 12 GLY None None
None 13 TYR None None
None 14 ARG None None
None 15 ARG None None
None 16 ASN None None
None 17 VAL None None
None 18 GLY None None
None 19 ILE None None
None 20 CYS None None
None 21 LEU None None
None 22 MET None None
None 23 ASN None None
None 24 ASN None None
None 25 ASP None None
None 26 LYS None None
None 27 LYS None None
None 28 ILE None None
None 29 PHE None None
None 30 ALA None None
None 31 ALA None None
None 32 SER None None
None 33 ARG None None
None 34 LEU None None
None 35 ASP None None
None 36 ILE None None
None 37 PRO None None
None 38 ASP None None
None 39 ALA None None
None 40 TRP None None
None 41 GLN None None
None 42 MET None None
None 43 PRO None None
None 44 GLN None None
None 45 GLY None None
None 46 GLY None None
None 47 ILE None None
None 48 ASP None None
None 49 GLU None None
None 50 GLY None None
None 51 GLU None None
None 52 ASP None None
None 53 PRO None None
None 54 ARG None None
None 55 ASN None None
None 56 ALA None None
None 57 ALA None None
None 58 ILE None None
None 59 ARG None None
None 60 GLU None None
None 61 LEU None None
None 62 ARG None None
None 63 GLU None None
None 64 GLU None None
None 65 THR None None
None 66 GLY None None
None 67 VAL None None
None 68 THR None None
None 69 SER None None
None 70 ALA None None
None 71 GLU None None
None 72 VAL None None
None 73 ILE None None
None 74 ALA None None
None 75 GLU None None
None 76 VAL None None
None 77 PRO None None
None 78 TYR None None
None 79 TRP None None
None 80 LEU None None
None 81 THR None None
None 82 TYR None None
None 83 ASP None None
None 84 PHE None None
None 85 PRO None None
None 86 PRO None None
None 87 LYS None None
None 88 VAL None None
None 89 ARG None None
None 90 GLU None None
None 91 LYS None None
None 92 LEU None None
None 93 ASN None None
None 94 ILE None None
None 95 GLN None None
None 96 TRP None None
None 97 GLY None None
None 98 SER None None
None 99 ASP None None
None 100 TRP None None
None 101 LYS None None
None 102 GLY None None
None 103 GLN None None
None 104 ALA None None
None 105 GLN None None
None 106 LYS None None
None 107 TRP None None
None 108 PHE None None
None 109 LEU None None
None 110 PHE None None
None 111 LYS None None
None 112 PHE None None
None 113 THR None None
None 114 GLY None None
None 115 GLN None None
None 116 ASP None None
None 117 GLN None None
None 118 GLU None None
None 119 ILE None None
None 120 ASN None None
None 121 LEU None None
None 122 LEU None None
None 123 GLY None None
None 124 ASP None None
None 125 GLY None None
None 126 SER None None
None 127 GLU None None
None 128 LYS None None
None 129 PRO None None
None 130 GLU None None
None 131 PHE None None
None 132 GLY None None
None 133 GLU None None
None 134 TRP None None
None 135 SER None None
None 136 TRP None None
None 137 VAL None None
None 138 THR None None
None 139 PRO None None
None 140 GLU None None
None 141 GLN None None
None 142 LEU None None
None 143 ILE None None
None 144 ASP None None
None 145 LEU None None
None 146 THR None None
None 147 VAL None None
None 148 GLU None None
None 149 PHE None None
None 150 LYS None None
None 151 LYS None None
None 152 PRO None None
None 153 VAL None None
None 154 TYR None None
None 155 LYS None None
None 156 GLU None None
None 157 VAL None None
None 158 LEU None None
None 159 SER None None
None 160 VAL None None
None 161 PHE None None
None 162 ALA None None
None 163 PRO None None
None 164 HIS None None
None 165 LEU None None
relax> structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir='/sw/lib/relax-py25/test_suite/shared_data/structures', model=1,
parser='scientific')
Scientific Python PDB parser.
Loading structure 1 from the PDB file.
Structure('/sw/lib/relax-py25/test_suite/shared_data/structures/Ap4Aase_res1-12.pdb',
model=1):
Peptide chain of length 12
relax> structure.load_spins(spin_id='@N', ave_pos=True)
Adding the following spins to the relax data store.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY 1 N
None 2 PRO 11 N
None 3 LEU 28 N
None 4 GLY 51 N
None 5 SER 59 N
None 6 MET 71 N
None 7 ASP 91 N
None 8 SER 104 N
None 9 PRO 116 N
None 10 PRO 133 N
None 11 GLU 150 N
None 12 GLY 167 N
relax> structure.vectors(attached='H', spin_id=None, struct_index=None,
verbosity=1, ave=True, unit=True)
Extracting vectors from the single structure.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: No attached atom could be found (atom ID ':1@1&@N').
RelaxWarning: No attached atom could be found (atom ID ':2@11&@N').
Extracted N-H vectors for ':3@28&@N'.
Extracted N-H vectors for ':4@51&@N'.
Extracted N-H vectors for ':5@59&@N'.
Extracted N-H vectors for ':6@71&@N'.
Extracted N-H vectors for ':7@91&@N'.
Extracted N-H vectors for ':8@104&@N'.
RelaxWarning: No attached atom could be found (atom ID ':9@116&@N').
RelaxWarning: No attached atom could be found (atom ID ':10@133&@N').
Extracted N-H vectors for ':11@150&@N'.
Extracted N-H vectors for ':12@167&@N'.
RelaxWarning: Either the spin number or name must be set for the spin ':13'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':14'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':15'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':16'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':17'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':18'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':19'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':20'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':21'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':22'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':23'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':24'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':25'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':26'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':27'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':28'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':29'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':30'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':31'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':32'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':33'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':34'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':35'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':36'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':37'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':38'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':39'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':40'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':41'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':42'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':43'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':44'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':45'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':46'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':47'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':48'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':49'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':50'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':51'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':52'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':53'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':54'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':55'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':56'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':57'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':58'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':59'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':60'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':61'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':62'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':63'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':64'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':65'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':66'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':67'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':68'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':69'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':70'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':71'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':72'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':73'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':74'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':75'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':76'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':77'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':78'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':79'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':80'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':81'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':82'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':83'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':84'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':85'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':86'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':87'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':88'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':89'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':90'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':91'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':92'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':93'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':94'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':95'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':96'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':97'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':98'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':99'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':100'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':101'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':102'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':103'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':104'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':105'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':106'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':107'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':108'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':109'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':110'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':111'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':112'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':113'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':114'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':115'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':116'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':117'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':118'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':119'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':120'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':121'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':122'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':123'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':124'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':125'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':126'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':127'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':128'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':129'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':130'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':131'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':132'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':133'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':134'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':135'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':136'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':137'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':138'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':139'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':140'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':141'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':142'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':143'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':144'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':145'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':146'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':147'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':148'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':149'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':150'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':151'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':152'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':153'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':154'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':155'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':156'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':157'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':158'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':159'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':160'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':161'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':162'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':163'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':164'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':165'
to identify the corresponding atom in the structure.
relax> diffusion_tensor.init(params=(16980000.0, 14170000.0,
67.174000000000007, -83.718000000000004), time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=3, spheroid_type=None, fixed=True)
relax> sequence.display(sep=None, mol_name_flag=True, res_num_flag=True,
res_name_flag=True, spin_num_flag=True, spin_name_flag=True)
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY 1 N
None 2 PRO 11 N
None 3 LEU 28 N
None 4 GLY 51 N
None 5 SER 59 N
None 6 MET 71 N
None 7 ASP 91 N
None 8 SER 104 N
None 9 PRO 116 N
None 10 PRO 133 N
None 11 GLU 150 N
None 12 GLY 167 N
None 13 TYR None None
None 14 ARG None None
None 15 ARG None None
None 16 ASN None None
None 17 VAL None None
None 18 GLY None None
None 19 ILE None None
None 20 CYS None None
None 21 LEU None None
None 22 MET None None
None 23 ASN None None
None 24 ASN None None
None 25 ASP None None
None 26 LYS None None
None 27 LYS None None
None 28 ILE None None
None 29 PHE None None
None 30 ALA None None
None 31 ALA None None
None 32 SER None None
None 33 ARG None None
None 34 LEU None None
None 35 ASP None None
None 36 ILE None None
None 37 PRO None None
None 38 ASP None None
None 39 ALA None None
None 40 TRP None None
None 41 GLN None None
None 42 MET None None
None 43 PRO None None
None 44 GLN None None
None 45 GLY None None
None 46 GLY None None
None 47 ILE None None
None 48 ASP None None
None 49 GLU None None
None 50 GLY None None
None 51 GLU None None
None 52 ASP None None
None 53 PRO None None
None 54 ARG None None
None 55 ASN None None
None 56 ALA None None
None 57 ALA None None
None 58 ILE None None
None 59 ARG None None
None 60 GLU None None
None 61 LEU None None
None 62 ARG None None
None 63 GLU None None
None 64 GLU None None
None 65 THR None None
None 66 GLY None None
None 67 VAL None None
None 68 THR None None
None 69 SER None None
None 70 ALA None None
None 71 GLU None None
None 72 VAL None None
None 73 ILE None None
None 74 ALA None None
None 75 GLU None None
None 76 VAL None None
None 77 PRO None None
None 78 TYR None None
None 79 TRP None None
None 80 LEU None None
None 81 THR None None
None 82 TYR None None
None 83 ASP None None
None 84 PHE None None
None 85 PRO None None
None 86 PRO None None
None 87 LYS None None
None 88 VAL None None
None 89 ARG None None
None 90 GLU None None
None 91 LYS None None
None 92 LEU None None
None 93 ASN None None
None 94 ILE None None
None 95 GLN None None
None 96 TRP None None
None 97 GLY None None
None 98 SER None None
None 99 ASP None None
None 100 TRP None None
None 101 LYS None None
None 102 GLY None None
None 103 GLN None None
None 104 ALA None None
None 105 GLN None None
None 106 LYS None None
None 107 TRP None None
None 108 PHE None None
None 109 LEU None None
None 110 PHE None None
None 111 LYS None None
None 112 PHE None None
None 113 THR None None
None 114 GLY None None
None 115 GLN None None
None 116 ASP None None
None 117 GLN None None
None 118 GLU None None
None 119 ILE None None
None 120 ASN None None
None 121 LEU None None
None 122 LEU None None
None 123 GLY None None
None 124 ASP None None
None 125 GLY None None
None 126 SER None None
None 127 GLU None None
None 128 LYS None None
None 129 PRO None None
None 130 GLU None None
None 131 PHE None None
None 132 GLY None None
None 133 GLU None None
None 134 TRP None None
None 135 SER None None
None 136 TRP None None
None 137 VAL None None
None 138 THR None None
None 139 PRO None None
None 140 GLU None None
None 141 GLN None None
None 142 LEU None None
None 143 ILE None None
None 144 ASP None None
None 145 LEU None None
None 146 THR None None
None 147 VAL None None
None 148 GLU None None
None 149 PHE None None
None 150 LYS None None
None 151 LYS None None
None 152 PRO None None
None 153 VAL None None
None 154 TYR None None
None 155 LYS None None
None 156 GLU None None
None 157 VAL None None
None 158 LEU None None
None 159 SER None None
None 160 VAL None None
None 161 PHE None None
None 162 ALA None None
None 163 PRO None None
None 164 HIS None None
None 165 LEU None None
relax> angle_diff_frame()
RelaxWarning: No angles could be calculated for the spin ':1&:GLY@1&@N'.
RelaxWarning: No angles could be calculated for the spin ':2&:PRO@11&@N'.
RelaxWarning: No angles could be calculated for the spin ':9&:PRO@116&@N'.
RelaxWarning: No angles could be calculated for the spin ':10&:PRO@133&@N'.
RelaxWarning: No angles could be calculated for the spin ':13&:TYR'.
RelaxWarning: No angles could be calculated for the spin ':14&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':15&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':16&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':17&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':18&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':19&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':20&:CYS'.
RelaxWarning: No angles could be calculated for the spin ':21&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':22&:MET'.
RelaxWarning: No angles could be calculated for the spin ':23&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':24&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':25&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':26&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':27&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':28&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':29&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':30&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':31&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':32&:SER'.
RelaxWarning: No angles could be calculated for the spin ':33&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':34&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':35&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':36&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':37&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':38&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':39&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':40&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':41&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':42&:MET'.
RelaxWarning: No angles could be calculated for the spin ':43&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':44&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':45&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':46&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':47&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':48&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':49&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':50&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':51&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':52&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':53&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':54&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':55&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':56&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':57&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':58&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':59&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':60&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':61&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':62&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':63&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':64&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':65&:THR'.
RelaxWarning: No angles could be calculated for the spin ':66&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':67&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':68&:THR'.
RelaxWarning: No angles could be calculated for the spin ':69&:SER'.
RelaxWarning: No angles could be calculated for the spin ':70&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':71&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':72&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':73&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':74&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':75&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':76&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':77&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':78&:TYR'.
RelaxWarning: No angles could be calculated for the spin ':79&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':80&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':81&:THR'.
RelaxWarning: No angles could be calculated for the spin ':82&:TYR'.
RelaxWarning: No angles could be calculated for the spin ':83&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':84&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':85&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':86&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':87&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':88&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':89&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':90&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':91&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':92&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':93&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':94&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':95&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':96&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':97&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':98&:SER'.
RelaxWarning: No angles could be calculated for the spin ':99&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':100&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':101&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':102&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':103&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':104&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':105&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':106&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':107&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':108&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':109&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':110&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':111&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':112&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':113&:THR'.
RelaxWarning: No angles could be calculated for the spin ':114&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':115&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':116&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':117&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':118&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':119&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':120&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':121&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':122&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':123&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':124&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':125&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':126&:SER'.
RelaxWarning: No angles could be calculated for the spin ':127&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':128&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':129&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':130&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':131&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':132&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':133&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':134&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':135&:SER'.
RelaxWarning: No angles could be calculated for the spin ':136&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':137&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':138&:THR'.
RelaxWarning: No angles could be calculated for the spin ':139&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':140&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':141&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':142&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':143&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':144&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':145&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':146&:THR'.
RelaxWarning: No angles could be calculated for the spin ':147&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':148&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':149&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':150&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':151&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':152&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':153&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':154&:TYR'.
RelaxWarning: No angles could be calculated for the spin ':155&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':156&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':157&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':158&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':159&:SER'.
RelaxWarning: No angles could be calculated for the spin ':160&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':161&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':162&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':163&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':164&:HIS'.
RelaxWarning: No angles could be calculated for the spin ':165&:LEU'.
Class containing all the spin system specific data.
Objects:
element: 'N'
name: 'N'
num: 1
pos: array([ 8.442, 10.188, 6.302])
select: True
Class containing all the spin system specific data.
Objects:
element: 'N'
name: 'N'
num: 11
pos: array([ 5.613, 8.385, 7.943])
select: True
Class containing all the spin system specific data.
Objects:
alpha: 2.8102691247870468
attached_atom: 'H'
element: 'N'
name: 'N'
num: 28
pos: array([ 4.074, 6.099, 5.719])
select: True
xh_vect: array([ 0.40899187, -0.80574458, 0.42837054])
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/angles.py", line 104, in
test_angles
self.assertAlmostEqual(cdp.mol[0].res[i].spin[0].xh_vect[j],
xh_vects[i][j])
AssertionError: 0.40899187042469931 != -1.6863286833629661e+272 within 7
places
======================================================================
FAIL: Constrained BFGS opt, backtracking line search {S2=0.970, te=2048,
Rex=0.149}
----------------------------------------------------------------------
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Re: [bug #12573] FAIL: Constrained BFGS opt, backtracking line search {S2=0.970, te=2048 Rex=0.149}