/**
* $outfile will be overwritten.
* $cnit is an array of CNIT codes for the residues that were processed.
*/
function makeSswingKin($pdb1, $pdb2, $outfile, $cnit)
{
if (file_exists($outfile)) {
unlink($outfile);
}
$stats = describePdbStats(pdbstat($pdb1), false);
$h = fopen($outfile, 'a');
fwrite($h, "@text\n");
fwrite($h, "Sidechains have been refit by SSWING. Details of the input file:\n\n");
foreach ($stats as $stat) {
fwrite($h, "[+] {$stat}\n");
}
fwrite($h, "@kinemage 1\n");
// Calculate views for each residue in CNIT
$ctr = computeResCenters($pdb1);
foreach ($cnit as $res) {
$i++;
$c = $ctr[$res];
fwrite($h, "@{$i}viewid {{$res}}\n@{$i}span 12\n@{$i}zslab 100\n@{$i}center {$c['x']} {$c['y']} {$c['z']}\n");
}
fclose($h);
exec("prekin -quiet -append -animate -onegroup -show 'mc,sc(peach),ca,hy,ht,wa' {$pdb1} >> {$outfile}");
exec("phenix.probe -quiet -noticks -nogroup -self 'alta' {$pdb1} >> {$outfile}");
//exec("probe -quiet -noticks -nogroup -self 'alta' $pdb1 >> $outfile");
exec("prekin -quiet -append -animate -onegroup -show 'mc,sc(sky),ca,hy,ht,wa' {$pdb2} >> {$outfile}");
exec("phenix.probe -quiet -noticks -nogroup -self 'alta' {$pdb2} >> {$outfile}");
//exec("probe -quiet -noticks -nogroup -self 'alta' $pdb2 >> $outfile");
}
function onEditPDB()
{
$req = $_REQUEST;
//if($req['cmd'] == 'Cancel')
if ($req['cmd'] == 'Go back') {
pageGoto("editpdb_setup1.php");
return;
}
// Otherwise, moving forward:
$oldID = $req['modelID'];
$oldModel = $_SESSION['models'][$oldID];
$inpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $oldModel['pdb'];
$newModel = createModel($oldID . "_edit");
$newID = $newModel['id'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
$s = "";
if (is_array($req['removechain']) && count($req['removechain']) > 0) {
removeChains($inpath, $outpath, $req['removechain']);
$s .= "<p>You created {$newModel['pdb']} by removing chain(s) " . implode(', ', $req['removechain']) . " from {$oldModel['pdb']}.\n";
mpLog("editpdb:Removed chains from a PDB file");
} else {
copy($inpath, $outpath);
}
$resolu = $req['resolution'] + 0;
$oldRes = $oldModel['stats']['resolution'] + 0;
if ($resolu && ($oldRes == 0 || $oldRes != $resolu)) {
$remark2 = sprintf("REMARK 2 \nREMARK 2 RESOLUTION. %.2f ANGSTROMS. \n", $resolu);
replacePdbRemark($outpath, $remark2, 2);
$s .= "<p>You manually set the resolution for {$newModel['pdb']}.\n";
mpLog("editpdb:Changed/set resolution for a PDB file");
}
if ($req['removeHs']) {
$newModel = createModel($oldID . "_trimmed");
$newID = $newModel['id'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
reduceTrim($inpath, $outpath);
$s .= "<p>You created {$newModel['pdb']} by removing hydrogens from {$oldModel['pdb']}.\n";
mpLog("editpdb:Removed hydrogens from a PDB file");
}
$newModel['stats'] = pdbstat($outpath);
$newModel['history'] = "Edited {$oldModel['pdb']}";
$newModel['isUserSupplied'] = $oldModel['isUserSupplied'];
$_SESSION['models'][$newID] = $newModel;
$_SESSION['lastUsedModelID'] = $newID;
// this is now the current model
$details = describePdbStats($newModel['stats'], true);
$s .= "<ul>\n";
foreach ($details as $detail) {
$s .= "<li>{$detail}</li>\n";
}
$s .= "</ul>\n";
$entrynum = addLabbookEntry("Created PDB file {$newModel['pdb']}", $s, "{$oldID}|{$newID}", "auto", "scissors.png");
pageGoto("generic_done.php", array('labbookEntry' => $entrynum));
}
/**
* $context['modelID'] - the ID of the model the user will work with
*/
function display($context)
{
echo $this->pageHeader("Visualize interface contacts");
$modelID = $context['modelID'];
$model = $_SESSION['models'][$modelID];
// These lines create an HTML form that will call onRunProbe() to be called
// when the user clicks the submit button. onRunProbe() is declared below.
echo makeEventForm("onRunProbe");
echo "<input type='hidden' name='modelID' value='{$modelID}'>\n";
echo "<h3>Choose Probe options:</h3>";
?>
<table border='0' width='100%' cellspacing='0' cellpadding='4'><tr align='left' valign='top'>
<td>
<p>Type(s) of output: <select name="output_type">
<option value='both'>kinemage and list of contacts</option>
<option value='kin'>kinemage only</option>
<option value='list'>list of contacts only</option>
</select>
<p>Mode of action: <select name="probe_mode">
<option value="both" selected>both (src <=> targ)</option>
<option value="once">once (src -> targ)</option>
<option value="self">self (src -> src)</option>
<option value="out">out (src -> solvent)</option>
</select>
<p>Remove dots up to <select name="remove_dist">
<option value="4" selected>4</option>
<option value="3">3</option>
<option value="2">2</option>
<option value="1">1</option>
</select> bonds away
<p>Color dots <select name="color_by">
<option value="gap" selected>by gap/overlap distance (cool to warm)</option>
<option value="atom">by element (CPK colors)</option>
<option value="base">by nucleic acid base type</option>
<option value="gray">solid gray (for -out only)</option>
<option value="">[suggest other solid colors for -out using Feedback]</option>
</select>
<p><input type="checkbox" name="show_clashes" value="1" checked> Dots for clashes
<br><input type="checkbox" name="show_hbonds" value="1" checked> Dots for H-bonds
<br><input type="checkbox" name="show_vdw" value="1" checked> Dots for van der Waals contacts
<br><input type="checkbox" name="show_mc" value="1" checked> Mainchain-mainchain dots
<br><input type="checkbox" name="show_hets" value="1" checked> Dots to hets
<br><input type="checkbox" name="show_wat" value="1" checked> Dots to waters
<br><input type="checkbox" name="wat2wat" value="1"> Dots between waters
<br><input type="checkbox" name="alta" value="1" checked> 'A' conformation only
<br><input type="checkbox" name="blt40" value="1"> Atoms with B<40 only
<br><input type="checkbox" name="ogt33" value="1"> Atoms with >33% occupancy only
<br><input type='checkbox' name='drop_flag' value='1'> Non-selected atoms don't exist (-drop)
<br><input type="checkbox" name="elem_masters" value="1"> Masters for each element (C,H,O,...)
<p>Output file: <?php
echo $model['prefix'];
?>
<input type="text" name="kin_suffix" value="interface" size=10 maxlength=20>.kin
<br><small>(Will be overwritten, alphanumeric only, no spaces or symbols, <20 chars)</small>
</td>
<td width='20'><!-- ##################################################################### --></td>
<td>
Just as a reminder:
<ul>
<?php
$details = describePdbStats($model['stats'], true);
foreach ($details as $detail) {
echo "<li>{$detail}</li>\n";
}
?>
</ul>
<p><table border=1 width=100% cellspacing=0 cellpadding=4>
<tr align=center>
<td></td>
<td><b>"Src" pattern</b></td>
<td><b>"Targ" pattern</b></td>
</tr>
<tr align=center>
<td><b>Protein</b></small></td>
<td><input type=checkbox name="src_prot" value="protein" checked></td>
<td><input type=checkbox name="targ_prot" value="protein" checked></td>
</tr>
<tr align=center>
<td><b>DNA, RNA</b></small></td>
<td><input type=checkbox name="src_nucacid" value="dna,rna" checked></td>
<td><input type=checkbox name="targ_nucacid" value="dna,rna" checked></td>
</tr>
<tr align=center>
<td><b>Hets</b></td>
<td><input type=checkbox name="src_hets" value="het" checked></td>
<td><input type=checkbox name="targ_hets" value="het" checked></td>
</tr>
<tr align=center>
<td><b>Waters</b></td>
<td><input type=checkbox name="src_waters" value="water" checked></td>
<td><input type=checkbox name="targ_waters" value="water" checked></td>
</tr>
<tr align=center>
<td colspan=3 bgcolor=#999999>
<b>- AND -</b>
<br><small>(i.e., the logical intersection of the top half and the bottom half)</small>
</td>
</tr>
<?php
foreach ($model['stats']['chainids'] as $cid) {
echo "<tr align='center'>\n";
echo "<td><b>Chain "{$cid}"</b></td>\n";
echo "<td><input type='checkbox' name='src_chains[{$cid}]' value='{$cid}' checked></td>\n";
echo "<td><input type='checkbox' name='targ_chains[{$cid}]' value='{$cid}' checked></td>\n";
echo "</tr>\n";
}
?>
</table>
</td>
</tr></table>
<p>Note that some steps are processor-intensive and may require several minutes to complete. Please be patient.
<?php
echo "<p><table width='100%' border='0'><tr>\n";
echo "<td><input type='submit' name='cmd' value='Run Probe >'></td>\n";
echo "<td align='right'><input type='submit' name='cmd' value='Go back'></td>\n";
echo "</tr></table></p></form>\n";
// Note the explicit </form> to end the form!
?>
<hr>
<div class='help_info'>
<h4>Visualizing interface contacts</h4>
<i>TODO: Help text about interfaces and Probe goes here</i>
</div>
<?php
echo $this->pageFooter();
}
/**
* $infiles is an array of one or more PDB files to process
* $outfile will be overwritten.
* $opt controls what will be output. Each key below maps to a boolean:
* Bscale color scale by B-factor
* Qscale color scale by occupancy
* altconf alternate conformations
* ribbons ribbons rainbow colored N to C
* rama Ramachandran outliers
* rota rotamer outliers
* geom Bond length and angle geometry
* cbdev C-beta deviations greater than 0.25A
* pperp phosphate-base perpendicular outliers
* clashdots small and bad overlap dots
* hbdots H-bond dots
* vdwdots van der Waals (contact) dots
* $viewRes is a list of 9-char "CNIT" names of residues for which there should views
* (e.g. outliers that someone should inspect, etc.)
* $nmrConstraints is optional, and if present will generate lines for violated NOEs
* $clashLimit is an option for probe, to set the clash cutoff to something different than -0.4
*/
function makeMulticritKin2($infiles, $outfile, $opt, $viewRes = array(), $nmrConstraints = null, $clashLimit = null)
{
if (file_exists($outfile)) {
if (!unlink($outfile)) {
echo "delete .kin file failed!\n";
}
}
$pdbstats = pdbstat(reset($infiles));
$stats = describePdbStats($pdbstats, false);
$h = fopen($outfile, 'a');
fwrite($h, "@text\n");
foreach ($stats as $stat) {
fwrite($h, "[+] {$stat}\n");
}
$isMultiModel = count($infiles) > 1;
if ($isMultiModel) {
fwrite($h, "Statistics for first model only; " . count($infiles) . " total models included in kinemage.\n");
}
// For Dave and Jane: version numbers!
// This *is* useful for looking at old multikins...
fwrite($h, "\n\n\n");
fwrite($h, exec("prekin -version") . "\n");
$reduce_help = explode("\n", shell_exec("phenix.reduce -help 2>&1"));
//$reduce_help = explode("\n", shell_exec("reduce -help 2>&1"));
fwrite($h, "{$reduce_help['0']}\n");
//fwrite($h, "Probe: ".exec("probe -version")."\n"); -- Probe puts its version in the @caption
fwrite($h, "@kinemage 1\n");
fwrite($h, "@onewidth\n");
fclose($h);
$view_info = makeResidueViews(reset($infiles), $outfile, $viewRes);
#echo "made residue views OK\n";
foreach ($infiles as $infile) {
// Animate is used even for single models, so they can be appended later.
//echo("prekin -quiet -lots -append -animate -onegroup $infile >> $outfile\n");
if (!$_SESSION['useSEGID']) {
exec("prekin -quiet -lots -append -animate -onegroup {$infile} >> {$outfile}");
} else {
exec("prekin -quiet -segid -lots -append -animate -onegroup {$infile} >> {$outfile}");
}
#echo "before ribbon options\n";
if ($opt['ribbons']) {
makeRainbowRibbons($infile, $outfile);
//rainbow ribbons are now default, since change in refinement practices has made b-factor ribbons less useful
//consider adding ribbon type selection to user options
//if($isMultiModel) makeRainbowRibbons($infile, $outfile);
//else makeBfactorRibbons($infile, $outfile);
}
#echo "after ribbon options\n";
if ($nmrConstraints) {
exec("noe-display -cv -s viol -ds+ -fs -k {$infile} {$nmrConstraints} < /dev/null >> {$outfile}");
}
if ($opt['clashdots'] || $opt['hbdots'] || $opt['vdwdots']) {
#echo "making Probe Dots...\n";
if ($clashLimit == null) {
makeProbeDots($infile, $outfile, $opt['hbdots'], $opt['vdwdots'], $opt['clashdots']);
} else {
makeProbeDots($infile, $outfile, $opt['hbdots'], $opt['vdwdots'], $opt['clashdots'], $clashLimit);
}
#echo "Probe dots OK\n";
}
if ($opt['omega']) {
#"making Cis Peptides...\n";
makeBadOmegaKin($infile, $outfile);
#"Cis Peptides OK\n";
}
if ($opt['rama']) {
#echo "making Rama...\n";
makeBadRamachandranKin($infile, $outfile);
#echo "Rama OK\n";
}
if ($opt['rota']) {
#"making Bad Rota...\n";
makeBadRotamerKin($infile, $outfile);
#"Bad Rota OK\n";
}
if ($opt['geom']) {
#"making Geom...\n";
makeBadGeomKin($infile, $outfile);
#"Geom OK\n";
}
if ($opt['cbdev']) {
#"making Cbeta...\n";
makeBadCbetaBalls($infile, $outfile);
#"Cbeta OK\n";
}
if ($opt['cablam']) {
#"making CaBLAM...\n";
makeBadCablamKin($infile, $outfile);
#"CaBLAM OK\n";
}
if ($opt['pperp']) {
#"Making BadPPerp...\n";
makeBadPPerpKin($infile, $outfile);
#"BadPPerp OK\n";
}
if ($opt['Bscale']) {
#"making Bfactor...\n";
makeBfactorScale($infile, $outfile);
#"Bfactor OK\n";
}
if ($opt['Qscale']) {
#"making Occupancy...\n";
makeOccupancyScale($infile, $outfile);
#"Occupancy OK\n";
}
if ($opt['altconf']) {
#"making Alts...\n";
makeAltConfKin($infile, $outfile);
#"Alts OK\n";
}
if ($view_info) {
#"making ViewMarkers...\n";
makeResidueViewMarkers($outfile, $view_info);
#"ViewMarkers OK\n";
}
#echo "make it through all options OK\n";
}
// KiNG allows us to do this to control what things are visible
$h = fopen($outfile, 'a');
fwrite($h, "@master {mainchain} off\n");
fwrite($h, "@master {sidechain} off\n");
if ($pdbstats['hydrogens'] > 0) {
fwrite($h, "@master {H's} off\n");
}
if ($pdbstats['waters'] > 0) {
fwrite($h, "@master {water} off\n");
}
fwrite($h, "@master {Calphas} on\n");
fwrite($h, "@master {Virtual BB} on\n");
// for protein + DNA/RNA structures
if ($opt['vdwdots']) {
fwrite($h, "@master {vdw contact} off\n");
}
if ($opt['clashdots']) {
fwrite($h, "@master {small overlap} off\n");
}
if ($opt['hbdots']) {
fwrite($h, "@master {H-bonds} off\n");
}
if ($opt['ribbons']) {
fwrite($h, "@master {ribbon} off\n");
}
if ($opt['Bscale']) {
fwrite($h, "@master {B factors} off\n");
}
if ($opt['Qscale']) {
fwrite($h, "@master {occupancy} off\n");
}
if ($opt['altconf'] && $pdbstats['all_alts'] > 0) {
fwrite($h, "@master {mc alt confs} off\n");
fwrite($h, "@master {sc alt confs} off\n");
}
fclose($h);
}
$s .= "<applet code='Magelet.class' archive='magejava.jar' width='150' height='150'>\n";
$s .= " <param name='kinemage' value='{$kinURL}/{$model['prefix']}thumbnail.kin'>\n";
$s .= " <param name='buttonpanel' value='no'>\n";
$s .= "</applet>\n";
$s .= "<center><small><a href='help/java.html' target='_blank'>Don't see anything?</a></i></small></center>\n";
$s .= "</div>\n";
if (count($idList) > 1) {
$ensemble = $_SESSION['ensembles'][$id];
$title = "Uploaded " . count($idList) . "-model ensemble as {$ensemble['pdb']}";
$s .= "Your file from {$fileSource} was uploaded as an ensemble of " . count($idList) . " separate models.\n";
$s .= "The following description applies to the first of these models, which is shown in the thumbnail kinemage:\n";
} else {
$title = "Uploaded PDB file as {$model['pdb']}";
$s .= "Your file from {$fileSource} was uploaded as {$model['pdb']}.\n";
}
$details = describePdbStats($model['stats'], true);
$s .= "<ul>\n";
foreach ($details as $detail) {
$s .= "<li>{$detail}</li>\n";
}
$s .= "</ul>\n";
$s .= $map_notebook_msg;
if ($model['stats']['originalInputH']) {
$cur = $_SESSION['lastUsedModelID'];
if (isset($_SESSION['ensembles'][$cur])) {
$orig = "the original ensemble (or individual model)";
} else {
foreach ($_SESSION['models'] as $id_m => $model_m) {
if ($_SESSION['lastUsedModelID'] != $id_m) {
$orig = $model_m['pdb'];
}
