Detail of

"; $query = "SELECT id FROM biomolecule WHERE pdbcode='$parameter';"; $result = pg_exec($link, $query); $row = pg_fetch_row($result); $biomoleculeId = $row[0]; if (!$biomoleculeId) { echo '

ERROR: internal error, PDB structure with PDB ID ' . $parameter . ' not found in database!

'; die(); } $query = "SELECT name, authors, method, datedeposition, daterelease, sequence, id FROM biomoleculeData WHERE biomoleculeId='$biomoleculeId';"; $result = pg_exec($link, $query); $row = pg_fetch_row($result); $biomoleculeDataId = $row[6]; echo '

'; 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 '"; 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 "

"; } elseif ($row[2] == "X-RAY DIFFRACTION"){ $query = "SELECT resolutionlow, resolutionhigh, method, temperature, ph, reflectionsall, reflectionsobs FROM methodXRayData WHERE biomoleculeDataId='$biomoleculeDataId';"; $result = pg_exec($link, $query); $row = pg_fetch_row($result); 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 "

"; } ?> 0) { 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 '

'; 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 ''; echo ''; $query = "SELECT residue.name, residue.position, shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist, chain.name, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN structureParameter ON structureParameter.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("StructureParameter", $_SESSION['highlightTables'])) && (in_array($row[15], $highlightResidues))) { echo ''; } echo "
ResidueShearStretchStaggerBucklePropellerOpeningShiftSlideRiseTiltRollTwist
'; } else { echo ''; } echo $parameter . "_" . $row[14] . "_" . $row[0] . $row[1] . '' . $row[2] . '' . $row[3] . '' . $row[4] . '' . $row[5] . '' . $row[6] . '' . $row[7] . '' . $row[8] . '' . $row[9] . '' . $row[10] . '' . $row[11] . '' . $row[12] . '' . $row[13] . '
"; echo '

'; if (!isset($written)) { echo '

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.

'; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, i1_i2, i1_i2Ring, i1_j2, i1_j2Ring, j1_i2, j1_i2Ring, j1_j2, j1_j2Ring, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN overlapArea ON overlapArea.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("OverlapArea", $_SESSION['highlightTables'])) && (in_array($row[11], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
Residuei1-i2i1-j2j1-i2j1-j2
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '(' . $row[4] . ')' . $row[5] . '(' . $row[6] . ')' . $row[7] . '(' . $row[8] . ')' . $row[9] . '(' . $row[10] . ')
"; echo '
'; 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

'; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, Ox, Oy, Oz, Nx, Ny, Nz, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN originMeanNormalVector ON originMeanNormalVector.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("OriginMeanNormalVector", $_SESSION['highlightTables'])) && (in_array($row[9], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
ResidueOxOyOzNxNyNz
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '' . $row[5] . '' . $row[6] . '' . $row[7] . '' . $row[8] . '
"; echo '
'; echo '

'; echo 'Local base-pair helical parameters
'; echo '

'; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, X_disp, Y_disp, h_Rise, Incl, Tip, h_Twist, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN helicalParameter ON helicalParameter.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("HelicalParameter", $_SESSION['highlightTables'])) && (in_array($row[9], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
ReisudeX-dispY-disph-RiseIncl.Tiph-Twist
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '' . $row[5] . '' . $row[6] . '' . $row[7] . '' . $row[8] . '
"; echo '
'; echo '

'; echo 'Classification of each dinucleotide step
'; echo '

'; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, Xp, Yp, Zp, XpH, YpH, ZpH, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN StepClassification ON StepClassification.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("StepClassification", $_SESSION['highlightTables'])) && (in_array($row[9], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
ResidueXpYpZpXpHYpHZpH
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '' . $row[5] . '' . $row[6] . '' . $row[7] . '' . $row[8] . '
"; echo '
'; 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

'; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, disp, angle, twist, rise, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN C1GlobalParameter ON C1GlobalParameter.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("C1GlobalParameter", $_SESSION['highlightTables'])) && (in_array($row[7], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
Residuedisp.angletwistrise
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '' . $row[5] . '' . $row[6] . '
"; echo '
'; echo '

'; echo 'Main chain and chi torsion angles
'; echo '

'; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, alpha, beta, gamma, delta, epsilon, zeta, chi, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN torsionAngle ON torsionAngle.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("TorsionAngle", $_SESSION['highlightTables'])) && (in_array($row[10], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
Residuealphabetagammadeltaepsilonzetachi
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '' . $row[5] . '' . $row[6] . '' . $row[7] . '' . $row[8] . '' . $row[9] . '
"; echo '
'; echo '

'; echo 'Sugar conformational parameters
'; echo 'tm: amplitude of pseudorotation of the sugar ring
P: phase angle of pseudorotation of the sugar ring

'; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, tm, P, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN sugarConformationalParameter ON sugarConformationalParameter.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("SugarConformationalParameter", $_SESSION['highlightTables'])) && (in_array($row[5], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
ResiduetmP
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '
"; echo '
'; echo '

'; echo 'Same strand P--P and C1\'--C1\' virtual bond distances
'; echo '

'; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, PP, C1C1, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN pCVirtualBondDistance ON pCVirtualBondDistance.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("PCVirtualBondDistance", $_SESSION['highlightTables'])) && (in_array($row[5], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
ResidueP--PC1\'--C1\'
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '
"; echo '
'; echo '

'; echo 'Helix radius
'; echo 'radial displacement of P, O4\', and C1\' atoms in local helix frame of each dimer

'; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, P, O4, C1 FROM chain JOIN residue ON chain.id=residue.chainid JOIN helixRadiusRadialDisplacement ON helixRadiusRadialDisplacement.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; echo ''; echo ''; } echo "
ResiduePO4C1
' . $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '' . $row[5] . '
"; echo '
'; echo '

'; echo 'Position and local helical axis vector
'; echo '

'; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; echo ''; $query = "SELECT residue.name, residue.position, chain.name, Px, Py, Pz, Hx, Hy, Hz, residue.id FROM chain JOIN residue ON chain.id=residue.chainid JOIN positionAndLocalHelicalAxisVector ON positionAndLocalHelicalAxisVector.residueId=residue.id WHERE biomoleculeId='$biomoleculeId' ORDER BY residue.position;"; $result = pg_exec($link, $query); while ($row = pg_fetch_row($result)) { $written="yes"; echo ''; if ((in_array("PositionAndLocalHelicalAxisVector", $_SESSION['highlightTables'])) && (in_array($row[9], $highlightResidues))) { echo ''; echo ''; echo ''; } echo "
ResiduePxPyPzHxHyHz
'; } else { echo ''; } echo $parameter . "_" . $row[2] . "_" . $row[0] . $row[1] . '' . $row[3] . '' . $row[4] . '' . $row[5] . '' . $row[6] . '' . $row[7] . '' . $row[8] . '
"; echo '
'; echo "

"; ?>