/**
* clash, rota, rama are from the corresponding loadXXX() functions
*/
function getEffectiveResolution($clash, $rota, $rama)
{
// Use of count(...) may occasionally lead to divide-by-zero if you have
// non-protein PDB files. I don't try to trap it b/c the PHP error msg
// then becomes a useful diagnostic. (Then $ro or $ra evaluates to unset,
// and so acts as zero in arithmetic expressions, FWIW.)
$cs = $clash['scoreAll'];
$ro = 100.0 * count(findRotaOutliers($rota)) / count($rota);
$ramaScore = array();
foreach ($rama as $r) {
$ramaScore[$r['eval']] += 1;
}
$ra = 100.0 - 100.0 * $ramaScore['Favored'] / count($rama);
//echo " cs=$cs, ro=$ro, ra=$ra ";
//return 0.4548*log(1+$cs) + 0.4205*log(1+$ro) + 0.3186*log(1+$ra) - 0.5001;
// We are now working based on a "best feasible structure for your resolution" scale,
// so all scores = 0 corresponds to a resolution of 0.5 A
//return 0.4548*log(1+$cs) + 0.4205*log(1+$ro) + 0.3186*log(1+$ra) + 0.5;
return 0.42574 * log(1 + $cs) + 0.32996 * log(1 + max(0, $ro - 1)) + 0.24979 * log(1 + max(0, $ra - 2)) + 0.5;
}
/**
* Composites the results of the find___Outliers() functions into a simple,
* non-redundant list of 9-char residues names (keys)
* and counts of outliers (values).
*/
function findAllOutliers($clash, $rama, $rota, $cbdev, $pperp)
{
$worst = array();
#$worst = array_merge($worst, findClashOutliers($clash));
#$worst = array_merge($worst, findRamaOutliers($rama));
#$worst = array_merge($worst, findRotaOutliers($rota));
#$worst = array_merge($worst, findCbetaOutliers($cbdev));
#$worst = array_merge($worst, findBasePhosPerpOutliers($pperp));
foreach (array(findClashOutliers($clash), findRamaOutliers($rama), findRotaOutliers($rota), findCbetaOutliers($cbdev), findBasePhosPerpOutliers($pperp)) as $criterion) {
if (is_array($criterion)) {
foreach ($criterion as $cnit => $dummy) {
$worst[$cnit] += 1;
}
}
}
ksort($worst);
// Put the residues into a sensible order
#return array_keys($worst);
return $worst;
}
/**
* $infiles array of single model PDB files to process
* $outfile will be overwritten with a kinemage
*/
function writeMultimodelChart($infiles, $outfile)
{
$infiles = array_values($infiles);
// re-indexes from 0 ... n-1
$clashes = array();
$clashOuts = array();
$clashCount = array();
$rotas = array();
$rotaOuts = array();
$rotaCount = array();
$ramas = array();
$ramaOuts = array();
$ramaCount = array();
$tmpfile = mpTempfile();
for ($i = 0; $i < count($infiles); $i++) {
runClashlist($infiles[$i], $tmpfile);
$clashes[$i] = loadClashlist($tmpfile);
$clashOuts[$i] = findClashOutliers($clashes[$i]);
foreach ($clashOuts[$i] as $cnit => $junk) {
$clashCount[$cnit] += 1;
}
runRotamer($infiles[$i], $tmpfile);
$rotas[$i] = loadRotamer($tmpfile);
$rotaOuts[$i] = findRotaOutliers($rotas[$i]);
foreach ($rotaOuts[$i] as $cnit => $junk) {
$rotaCount[$cnit] += 1;
}
runRamachandran($infiles[$i], $tmpfile);
$ramas[$i] = loadRamachandran($tmpfile);
$ramaOuts[$i] = findRamaOutliers($ramas[$i]);
foreach ($ramaOuts[$i] as $cnit => $junk) {
$ramaCount[$cnit] += 1;
}
}
$allRes = array_values(listResidues($infiles[0]));
// for now, assume all files have same res
$out = fopen($outfile, 'wb');
fwrite($out, "@kinemage 1\n");
fwrite($out, "@flatland\n");
fwrite($out, "@group {models} animate collapsable\n");
fwrite($out, "@labellist {res names}\n");
for ($j = 0; $j < count($allRes); $j++) {
fwrite($out, "{" . $allRes[$j] . "} 0 -{$j} 0\n");
}
fwrite($out, "@balllist {grid} radius= 0.02 nohighlight color= gray\n");
for ($j = 0; $j < count($allRes); $j++) {
for ($i = 0; $i < count($infiles); $i++) {
fwrite($out, "{} " . (-$i - 1) . " -{$j} 0\n");
}
}
for ($i = 0; $i < count($infiles); $i++) {
fwrite($out, "@subgroup {" . basename($infiles[$i]) . "} dominant\n");
fwrite($out, "@ringlist {clashes} master= {clashes} radius= 0.3 width= 2 color= hotpink\n");
for ($j = 0; $j < count($allRes); $j++) {
if ($clashOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} " . (-$i - 1) . " -{$j} 0\n");
}
}
fwrite($out, "@ringlist {rotamers} master= {rotamers} radius= 0.1 width= 2 color= gold\n");
for ($j = 0; $j < count($allRes); $j++) {
if ($rotaOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} " . (-$i - 1) . " -{$j} 0\n");
}
}
fwrite($out, "@ringlist {Ramachandran} master= {Ramachandran} radius= 0.2 width= 2 color= green\n");
for ($j = 0; $j < count($allRes); $j++) {
if ($ramaOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} " . (-$i - 1) . " -{$j} 0\n");
}
}
}
fwrite($out, "@group {criteria (rings)} animate collapsable\n");
fwrite($out, "@labellist {res names}\n");
for ($j = 0; $j < count($allRes); $j++) {
fwrite($out, "{" . $allRes[$j] . "} 0 -{$j} " . -0.1 * $i . "\n");
}
for ($i = 0; $i < count($infiles); $i++) {
fwrite($out, "@subgroup {" . basename($infiles[$i]) . "} dominant\n");
$xpos = 0;
fwrite($out, "@ringlist {clashes} radius= " . 0.5 * ($i + 1) / count($infiles) . " width= 1 color= hotpink\n");
$xpos -= 1.5;
for ($j = 0; $j < count($allRes); $j++) {
if ($clashOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} {$xpos} -{$j} " . -0.1 * $i . "\n");
}
}
fwrite($out, "@ringlist {rotamers} radius= " . 0.5 * ($i + 1) / count($infiles) . " width= 1 color= gold\n");
$xpos -= 1.5;
for ($j = 0; $j < count($allRes); $j++) {
if ($rotaOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} {$xpos} -{$j} " . -0.1 * $i . "\n");
}
}
fwrite($out, "@ringlist {Ramachandran} radius= " . 0.5 * ($i + 1) / count($infiles) . " width= 1 color= green\n");
$xpos -= 1.5;
for ($j = 0; $j < count($allRes); $j++) {
if ($ramaOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} {$xpos} -{$j} " . -0.1 * $i . "\n");
}
}
}
fwrite($out, "@group {criteria (lines)} animate collapsable\n");
fwrite($out, "@labellist {res names}\n");
for ($j = 0; $j < count($allRes); $j++) {
fwrite($out, "{" . $allRes[$j] . "} 0 -{$j} " . -0.1 * $i . "\n");
}
$xpos = 0;
fwrite($out, "@vectorlist {clashes} color= hotpink\n");
$xpos -= 1;
writeMultimodelChart_bars($out, $allRes, $clashCount, count($infiles), $xpos);
fwrite($out, "@vectorlist {rotamers} color= gold\n");
$xpos -= 1;
writeMultimodelChart_bars($out, $allRes, $rotaCount, count($infiles), $xpos);
fwrite($out, "@vectorlist {Ramachandran} color= green\n");
$xpos -= 1;
writeMultimodelChart_bars($out, $allRes, $ramaCount, count($infiles), $xpos);
fwrite($out, "@group {criteria (worms)} animate collapsable\n");
fwrite($out, "@labellist {res names}\n");
for ($j = 0; $j < count($allRes); $j++) {
fwrite($out, "{" . $allRes[$j] . "} 0 -{$j} " . -0.1 * $i . "\n");
}
$xpos = 0;
fwrite($out, "@trianglelist {clashes} color= hotpink\n");
$xpos -= 1;
writeMultimodelChart_boxes($out, $allRes, $clashCount, count($infiles), $xpos);
fwrite($out, "@trianglelist {rotamers} color= gold\n");
$xpos -= 1;
writeMultimodelChart_boxes($out, $allRes, $rotaCount, count($infiles), $xpos);
fwrite($out, "@trianglelist {Ramachandran} color= green\n");
$xpos -= 1;
writeMultimodelChart_boxes($out, $allRes, $ramaCount, count($infiles), $xpos);
fclose($out);
}
function makeChartKin($pdbname, $ChartKin)
{
$caption = "caption goes here";
$out = fopen($ChartKin, 'w');
fwrite($out, "@kinemage \n");
fwrite($out, " \n");
fwrite($out, " \n");
fwrite($out, "@onewidth \n");
fwrite($out, "@viewid {Overview} \n");
fwrite($out, "@zoom 1.00 \n");
fwrite($out, "@zslab 200 \n");
fwrite($out, "@ztran 0 \n");
fwrite($out, "@center -16.500 -11.500 0.122 \n");
fwrite($out, "@matrix \n");
fwrite($out, "1.000000 -0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -0.000000 1.000000 \n");
fwrite($out, "@master {Rotamer Outliers} \n");
fwrite($out, "@master {Rotamer % Outliers} \n");
fwrite($out, "@master {Global Measure Chart} \n");
fwrite($out, "@master {Residue Chart} \n");
fwrite($out, "@labellist {label} color= white master= {Global Measure Chart} nobutton \n");
fwrite($out, "{Resolution or Constrains per Residue}100.000 -30.000 0.000 \n");
fwrite($out, "{Value} -30.000 125.000 30.000 \n");
fwrite($out, "@vectorlist {edge} color= gray width= 1 master= {Global Measure Chart} nobutton \n");
fwrite($out, "{plot edge}P 0.000 250.000 0.000 \n");
fwrite($out, "{plot edge}0.000 0.000 0.000 \n");
fwrite($out, "{plot edge}250.000 0.000 0.000 \n");
fwrite($out, "{plot edge}250.000 250.000 0.000 \n");
fwrite($out, "{plot edge}0.000 250.000 0.000 \n");
fwrite($out, "@labellist {label} color= white master= {Residue Chart} nobutton \n");
fwrite($out, "{Model} 30.000 -30.000 -125.000 \n");
fwrite($out, "{Residue Number} -125.000 -30.000 30.000 \n");
fwrite($out, "@vectorlist {edge} color= gray width= 1 master= {Residue Chart} nobutton \n");
fwrite($out, "{plot edge}P -250.000 0.000 -250.000 \n");
fwrite($out, "{plot edge}0.000 0.000 -250.000 \n");
fwrite($out, "{plot edge}0.000 0.000 0.000 \n");
fwrite($out, "{plot edge}-250.000 0.000 0.000 \n");
fwrite($out, "{plot edge}-250.000 0.000 -250.000 \n");
fwrite($out, "@vectorlist {residue} color= gray width= 1 master= {Residue Chart} nobutton \n");
fwrite($out, "{tick}P 0.000 0.000 0.000 \n");
fwrite($out, "{\"}0.000 0.000 10.000 \n");
fwrite($out, "{\"}P -5.000 0.000 0.000 \n");
fwrite($out, "{\"}-5.000 0.000 5.000 \n");
fwrite($out, "{\"}P -10.000 0.000 0.000 \n");
fwrite($out, "{\"}-10.000 0.000 10.000 \n");
fwrite($out, "{\"}P -15.000 0.000 0.000 \n");
fwrite($out, "{\"}-15.000 0.000 5.000 \n");
fwrite($out, "{\"}P -20.000 0.000 0.000 \n");
fwrite($out, "{\"}-20.000 0.000 10.000 \n");
fwrite($out, "{\"}P -25.000 0.000 0.000 \n");
fwrite($out, "{\"}-25.000 0.000 5.000 \n");
fwrite($out, "{\"}P -30.000 0.000 0.000 \n");
fwrite($out, "{\"}-30.000 0.000 10.000 \n");
fwrite($out, "{\"}P -35.000 0.000 0.000 \n");
fwrite($out, "{\"}-35.000 0.000 5.000 \n");
fwrite($out, "{\"}P -40.000 0.000 0.000 \n");
fwrite($out, "{\"}-40.000 0.000 10.000 \n");
fwrite($out, "{\"}P -45.000 0.000 0.000 \n");
fwrite($out, "{\"}-45.000 0.000 5.000 \n");
fwrite($out, "{\"}P -50.000 0.000 0.000 \n");
fwrite($out, "{\"}-50.000 0.000 10.000 \n");
fwrite($out, "{\"}P -55.000 0.000 0.000 \n");
fwrite($out, "{\"}-55.000 0.000 5.000 \n");
fwrite($out, "{\"}P -60.000 0.000 0.000 \n");
fwrite($out, "{\"}-60.000 0.000 10.000 \n");
fwrite($out, "{\"}P -65.000 0.000 0.000 \n");
fwrite($out, "{\"}-65.000 0.000 5.000 \n");
fwrite($out, "{\"}P -70.000 0.000 0.000 \n");
fwrite($out, "{\"}-70.000 0.000 10.000 \n");
fwrite($out, "{\"}P -75.000 0.000 0.000 \n");
fwrite($out, "{\"}-75.000 0.000 5.000 \n");
fwrite($out, "{\"}P -80.000 0.000 0.000 \n");
fwrite($out, "{\"}-80.000 0.000 10.000 \n");
fwrite($out, "{\"}P -85.000 0.000 0.000 \n");
fwrite($out, "{\"}-85.000 0.000 5.000 \n");
fwrite($out, "{\"}P -90.000 0.000 0.000 \n");
fwrite($out, "{\"}-90.000 0.000 10.000 \n");
fwrite($out, "{\"}P -95.000 0.000 0.000 \n");
fwrite($out, "{\"}-95.000 0.000 5.000 \n");
fwrite($out, "{\"}P -100.000 0.000 0.000 \n");
fwrite($out, "{\"}-100.000 0.000 10.000 \n");
fwrite($out, "{\"}P -105.000 0.000 0.000 \n");
fwrite($out, "{\"}-105.000 0.000 5.000 \n");
fwrite($out, "{\"}P -110.000 0.000 0.000 \n");
fwrite($out, "{\"}-110.000 0.000 10.000 \n");
fwrite($out, "{\"}P -115.000 0.000 0.000 \n");
fwrite($out, "{\"}-115.000 0.000 5.000 \n");
fwrite($out, "{\"}P -120.000 0.000 0.000 \n");
fwrite($out, "{\"}-120.000 0.000 10.000 \n");
fwrite($out, "{\"}P -125.000 0.000 0.000 \n");
fwrite($out, "{\"}-125.000 0.000 5.000 \n");
fwrite($out, "{\"}P -130.000 0.000 0.000 \n");
fwrite($out, "{\"}-130.000 0.000 10.000 \n");
fwrite($out, "{\"}P -135.000 0.000 0.000 \n");
fwrite($out, "{\"}-135.000 0.000 5.000 \n");
fwrite($out, "{\"}P -140.000 0.000 0.000 \n");
fwrite($out, "{\"}-140.000 0.000 10.000 \n");
fwrite($out, "{\"}P -145.000 0.000 0.000 \n");
fwrite($out, "{\"}-145.000 0.000 5.000 \n");
fwrite($out, "{\"}P -150.000 0.000 0.000 \n");
fwrite($out, "{\"}-150.000 0.000 10.000 \n");
fwrite($out, "{\"}P -155.000 0.000 0.000 \n");
fwrite($out, "{\"}-155.000 0.000 5.000 \n");
fwrite($out, "{\"}P -160.000 0.000 0.000 \n");
fwrite($out, "{\"}-160.000 0.000 10.000 \n");
fwrite($out, "{\"}P -165.000 0.000 0.000 \n");
fwrite($out, "{\"}-165.000 0.000 5.000 \n");
fwrite($out, "{\"}P -170.000 0.000 0.000 \n");
fwrite($out, "{\"}-170.000 0.000 10.000 \n");
fwrite($out, "{\"}P -175.000 0.000 0.000 \n");
fwrite($out, "{\"}-175.000 0.000 5.000 \n");
fwrite($out, "{\"}P -180.000 0.000 0.000 \n");
fwrite($out, "{\"}-180.000 0.000 10.000 \n");
fwrite($out, "{\"}P -185.000 0.000 0.000 \n");
fwrite($out, "{\"}-185.000 0.000 5.000 \n");
fwrite($out, "{\"}P -190.000 0.000 0.000 \n");
fwrite($out, "{\"}-190.000 0.000 10.000 \n");
fwrite($out, "{\"}P -195.000 0.000 0.000 \n");
fwrite($out, "{\"}-195.000 0.000 5.000 \n");
fwrite($out, "{\"}P -200.000 0.000 0.000 \n");
fwrite($out, "{\"}-200.000 0.000 10.000 \n");
fwrite($out, "{\"}P -205.000 0.000 0.000 \n");
fwrite($out, "{\"}-205.000 0.000 5.000 \n");
fwrite($out, "{\"}P -210.000 0.000 0.000 \n");
fwrite($out, "{\"}-210.000 0.000 10.000 \n");
fwrite($out, "{\"}P -215.000 0.000 0.000 \n");
fwrite($out, "{\"}-215.000 0.000 5.000 \n");
fwrite($out, "{\"}P -220.000 0.000 0.000 \n");
fwrite($out, "{\"}-220.000 0.000 10.000 \n");
fwrite($out, "{\"}P -225.000 0.000 0.000 \n");
fwrite($out, "{\"}-225.000 0.000 5.000 \n");
fwrite($out, "{\"}P -230.000 0.000 0.000 \n");
fwrite($out, "{\"}-230.000 0.000 10.000 \n");
fwrite($out, "{\"}P -235.000 0.000 0.000 \n");
fwrite($out, "{\"}-235.000 0.000 5.000 \n");
fwrite($out, "{\"}P -240.000 0.000 0.000 \n");
fwrite($out, "{\"}-240.000 0.000 10.000 \n");
fwrite($out, "{\"}P -245.000 0.000 0.000 \n");
fwrite($out, "{\"}-245.000 0.000 5.000 \n");
fwrite($out, "{\"}P -250.000 0.000 0.000 \n");
fwrite($out, "{\"}-250.000 0.000 10.000 \n");
fwrite($out, "@vectorlist {Model} color= gray width= 1 master= {Residue Chart} nobutton \n");
fwrite($out, "{tick}P 0.000 0.000 0.000 \n");
fwrite($out, "{\"}10.000 0.000 0.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -10.000 \n");
fwrite($out, "{\"}5.000 0.000 -10.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -20.000 \n");
fwrite($out, "{\"}5.000 0.000 -20.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -30.000 \n");
fwrite($out, "{\"}5.000 0.000 -30.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -40.000 \n");
fwrite($out, "{\"}5.000 0.000 -40.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -50.000 \n");
fwrite($out, "{\"}10.000 0.000 -50.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -60.000 \n");
fwrite($out, "{\"}5.000 0.000 -60.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -70.000 \n");
fwrite($out, "{\"}5.000 0.000 -70.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -80.000 \n");
fwrite($out, "{\"}5.000 0.000 -80.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -90.000 \n");
fwrite($out, "{\"}5.000 0.000 -90.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -100.000 \n");
fwrite($out, "{\"}10.000 0.000 -100.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -110.000 \n");
fwrite($out, "{\"}5.000 0.000 -110.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -120.000 \n");
fwrite($out, "{\"}5.000 0.000 -120.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -130.000 \n");
fwrite($out, "{\"}5.000 0.000 -130.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -140.000 \n");
fwrite($out, "{\"}5.000 0.000 -140.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -150.000 \n");
fwrite($out, "{\"}10.000 0.000 -150.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -160.000 \n");
fwrite($out, "{\"}5.000 0.000 -160.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -170.000 \n");
fwrite($out, "{\"}5.000 0.000 -170.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -180.000 \n");
fwrite($out, "{\"}10.000 0.000 -180.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -190.000 \n");
fwrite($out, "{\"}5.000 0.000 -190.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -200.000 \n");
fwrite($out, "{\"}10.000 0.000 -200.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -210.000 \n");
fwrite($out, "{\"}5.000 0.000 -210.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -220.000 \n");
fwrite($out, "{\"}5.000 0.000 -220.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -230.000 \n");
fwrite($out, "{\"}5.000 0.000 -230.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -240.000 \n");
fwrite($out, "{\"}5.000 0.000 -240.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -250.000 \n");
fwrite($out, "{\"}10.000 0.000 -250.000 \n");
//for each pdb and iterate
//in the beginning.. there was a model!
$modelcounter = 1;
foreach ($pdbname as $pdb) {
//overall stats needed for each pdb file
// crystallographic resolution of the model
$stats = pdbstat($pdb);
$resolution = $stats['resolution'];
/*
$ConstPerRes =
// NMR constraints per Residue in the model
*/
//number of res in the model
$numRes = $stats['residues'];
// plotting of rotamer outliers along for each model along vs. residue number
fwrite($out, "@group {" . basename($pdb, ".pdb") . "} animate dominant \n");
// plot of rotamer outliers
fwrite($out, "@balllist {Rotamer Outliers} color= white radius= 0.5 master= {Rotamer Outliers} nohilite \n");
// create unique temp files in current directory
$tmp1 = tempnam(MP_BASE_DIR . "/tmp", 'graphtemp');
// calculations for rotamer data
runRotamer($pdb, $tmp1);
$rota = loadrotamer($tmp1);
//plotting rotamer outliers, determining the x (res), y (score), and z (model) values
//followed by writing them out in the balllist
$RotaOut = findRotaOutliers($rota);
// $RotaOut is the the list of outliers and their scores
foreach ($RotaOut as $ResName => $score) {
$x = $rota[$ResName]['resNum'] * -1.0;
$y = round($rota[$ResName]['scorePct'], 2);
$z = $modelcounter * -10.0;
// if x = 0, go to next one...
if ($x == 0) {
continue;
}
fwrite($out, "{" . basename($pdb, ".pdb") . " " . $ResName . "}{$x} {$y} {$z} \n");
}
// plotting % rotamer outlier data
// x is what you plot against, resolution / restraints per res etc
// y is the percentage of rotamer outliers in the entire model
// plots the model
$numRotaOut = count(findRotaOutliers($rota));
// can include a factor here
$percentoutlier = round($numRotaOut / $numRes * 100, 2);
// multiplication by 100 is the scaleing 'fudge' factor
$x = $resolution * 100;
// -10.00 another scaling factor
$z = $modelcounter * -10.0;
fwrite($out, "@balllist {Rotamer % Outliers} color= white radius= 1.0 master= {Rotamer % Outliers} nohilite \n");
fwrite($out, "{" . basename($pdb, ".pdb") . " " . $resolution . "A , " . $percentoutlier . "%" . "} {$x} {$percentoutlier} {$z} \n");
unlink($tmp1);
//change the Z number which gets multiplied (and hereafter we added another)
$modelcounter = $modelcounter + 1;
//end of the for each loop going through the PDB files
}
fclose($out);
}
