';
echo "Stucture PDB code: $parameter
";
echo "Name: " . $row[0] . "
";
echo "Authors: " . $row[1] . "
";
echo "Method: " . $row[2] . "
";
echo "Date of deposition: " . $row[3] . "
";
echo "Date of release: " . $row[4] . "
";
echo "Sequence: " . $row[5] . "
";
echo "
'; echo 'PDB lookup: ' . $parameter . ''; echo "
"; if ($row[2] == "SOLUTION NMR"){ $query = "SELECT fieldstrength, numberofmodels, temperature, pressure, ph, ionicstrenght FROM methodNMRData WHERE biomoleculeDataId='$biomoleculeDataId';"; $result = pg_exec($link, $query); $row = pg_fetch_row($result); echo '';
echo "NMR details
";
echo "Field strength: " . $row[0] . "
";
echo "Number of models: " . $row[1] . "
";
echo "Temperature: " . $row[2] . "
";
echo "Pressure: " . $row[3] . "
";
echo "pH: " . $row[4] . "
";
echo "Ionic Strenght: " . $row[5] . "
";
echo "
';
echo "X-Ray Diffraction details
";
echo "Resolution low: " . $row[0] . "
";
echo "Resolution high: " . $row[1] . "
";
echo "Method: " . $row[2] . "
";
echo "Temperature: " . $row[3] . "
";
echo "pH: " . $row[4] . "
";
echo "Reflections all: " . $row[5] . "
";
echo "Reflections obs: " . $row[6] . "
";
echo "
';
echo "Custom Fields
";
$query = "SELECT customName, customValue FROM customField WHERE biomoleculeId='$biomoleculeId'";
$result = pg_exec($link, $query);
while ($row = pg_fetch_row($result)){
echo "" . $row[0] . ": " . $row[1] . "
";
}
echo '
';
echo "Structure details
";
$query = "SELECT name, sequence, lenght FROM chain WHERE biomoleculeId='$biomoleculeId' ORDER BY name";
$result = pg_exec($link, $query);
while ($row = pg_fetch_row($result)){
echo "Chain: " . $row[0] . ", lenght " . $row[2] . ", sequence " . $row[1] . "
";
}
echo '
Pos | Name | Shear | Stretch | Stagger | Buckle | Propeller | Opening | Shift | Slide | Rise | Tilt | Roll | Twist |
' . $row[14] . '/' . $row[1] . ' | ' . $row[0] . ' | ' . $row[2] . ' | ' . $row[3] . ' | ' . $row[4] . ' | ' . $row[5] . ' | ' . $row[6] . ' | ' . $row[7] . ' | ' . $row[8] . ' | ' . $row[9] . ' | ' . $row[10] . ' | ' . $row[11] . ' | ' . $row[12] . ' | ' . $row[13] . ' |
WARNING: no base/step parameters found. The data probably wasn\'t parsed correctly.
'; } echo '';
echo 'Overlap area
';
echo 'Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step. Values in parentheses measure the overlap of base ring atoms only. Those outside parentheses include exocyclic atoms on the ring.
Pos | Name | '; echo 'i1-i2 | '; echo 'i1-j2 | '; echo 'j1-i2 | '; echo 'j1-j2 | '; echo '||||
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | (' . $row[4] . ') | ' . $row[5] . ' | (' . $row[6] . ') | ' . $row[7] . ' | (' . $row[8] . ') | ' . $row[9] . ' | (' . $row[10] . ') | '; echo '
';
echo 'Origin and mean normal vector
';
echo 'Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure
Pos | Name | '; echo 'Ox | '; echo 'Oy | '; echo 'Oz | '; echo 'Nx | '; echo 'Ny | '; echo 'Nz | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | ' . $row[5] . ' | ' . $row[6] . ' | ' . $row[7] . ' | ' . $row[8] . ' | '; echo '
';
echo 'Local base-pair helical parameters
';
echo '
Pos | Name | '; echo 'X-disp | '; echo 'Y-disp | '; echo 'h-Rise | '; echo 'Incl. | '; echo 'Tip | '; echo 'h-Twist | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | ' . $row[5] . ' | ' . $row[6] . ' | ' . $row[7] . ' | ' . $row[8] . ' | '; echo '
';
echo 'Classification of each dinucleotide step
';
echo '
Pos | Name | '; echo 'Xp | '; echo 'Yp | '; echo 'Zp | '; echo 'XpH | '; echo 'YpH | '; echo 'ZpH | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | ' . $row[5] . ' | ' . $row[6] . ' | ' . $row[7] . ' | ' . $row[8] . ' | '; echo '
';
echo 'Global parameters based on C1\'-C1\' vectors
';
echo 'disp.: displacement of the middle C1\'-C1\' point from the helix
angle: inclination between C1\'-C1\' vector and helix (subtracted from 90)
twist: helical twist angle between consecutive C1\'-C1\' vectors
rise: helical rise by projection of the vector connecting consecutive
C1\'-C1\' middle points onto the helical axis
Pos | Name | '; echo 'disp. | '; echo 'angle | '; echo 'twist | '; echo 'rise | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | ' . $row[5] . ' | ' . $row[6] . ' | '; echo '
';
echo 'Main chain and chi torsion angles
';
echo '
Pos | Name | '; echo 'alpha | '; echo 'beta | '; echo 'gamma | '; echo 'delta | '; echo 'epsilon | '; echo 'zeta | '; echo 'chi | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | ' . $row[5] . ' | ' . $row[6] . ' | ' . $row[7] . ' | ' . $row[8] . ' | ' . $row[9] . ' | '; echo '
';
echo 'Sugar conformational parameters
';
echo 'tm: amplitude of pseudorotation of the sugar ring
P: phase angle of pseudorotation of the sugar ring
Pos | Name | '; echo 'tm | '; echo 'P | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | '; echo '
';
echo 'Same strand P--P and C1\'--C1\' virtual bond distances
';
echo '
Pos | Name | '; echo 'P--P | '; echo 'C1\'--C1\' | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | '; echo '
';
echo 'Helix radius
';
echo 'radial displacement of P, O4\', and C1\' atoms in local helix frame of each dimer
Pos | Name | '; echo 'P | '; echo 'O4 | '; echo 'C1 | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | ' . $row[5] . ' | '; echo '
';
echo 'Position and local helical axis vector
';
echo '
Pos | Name | '; echo 'Px | '; echo 'Py | '; echo 'Pz | '; echo 'Hx | '; echo 'Hy | '; echo 'Hz | '; echo '
' . $row[2] . '/' . $row[1] . ' | ' . $row[0] . ' | '; echo '' . $row[3] . ' | ' . $row[4] . ' | ' . $row[5] . ' | ' . $row[6] . ' | ' . $row[7] . ' | ' . $row[8] . ' | '; echo '