Beispiel #1
0
    $tasks['regularize'] = "Regularize flipped N/Q/H geometry with <code>CCTBX</code> (if necessary)";
}
if ($_SESSION['bgjob']['makeFlipkin']) {
    $tasks['flipkin'] = "Create Asn/Gln and His <code>flipkin</code> kinemages";
}
setProgress($tasks, 'reduce');
$prereduceid = $_SESSION['lastUsedModelID'];
$newModel = createModel($modelID . "FH");
$outname = $newModel['pdb'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
if (!file_exists($outpath)) {
    mkdir($outpath, 0777);
}
// shouldn't ever happen, but might...
$outpath .= '/' . $outname;
reduceBuild($pdb, $outpath, $reduce_blength);
$newModel['stats'] = pdbstat($outpath);
$newModel['parent'] = $modelID;
$changes = decodeReduceUsermods($outpath);
// Check to see if any cliques couldn't be solved by looking for scores = -9.9e+99
// At the same time, check to see if anything at all was flipped...
$didnt_solve = $did_flip = false;
$n = count($changes[0]);
// How many changes are in the table?
for ($c = 0; $c < $n; $c++) {
    if ($changes[6][$c] == "-9.9e+99") {
        $didnt_solve = true;
    }
    if (!$did_flip && ($changes[4][$c] == "FLIP" || $changes[4][$c] == "CLS-FL")) {
        $did_flip = true;
    }
Beispiel #2
0
/**
* This is the uber-validation function that calls everything below.
* It is suited for use from either the web or command line interface.
* This only makes sense in terms of an active session.
*   modelID             ID code for model to process
*   opts                has the following keys mapped to boolean flags:
*     doKinemage        make the multi-criterion kinemage at all?
*       kinClashes      show clash dots?
*       kinHbonds       show H-bond dots?
*       kinContacts     show contact dots?
*       kinRama         show Rama outliers?
*       kinRota         show rotamer outliers?
*       kinGeom         show bond length and angle outliers?
*       kinCBdev        show C-beta deviations?
*       kinBaseP        show base-phosphate perpendiculars?
*       kinSuite        show RNA backbone conformational outliers?
*       kinAltConfs     show alternate conformations?
*       kinBfactor      show B-factor color model?
*       kinOccupancy    show occupancy color model?
*       kinRibbons      show ribbons?
*       kinForceViews   force running clashlist, etc to provide @views of bad spots?
*     doCharts          make the multi-criterion chart and other plots/tables/lists?
*       chartClashlist  run clashlistcluster?
*       chartRama       do Rama plots and analysis?
*       chartRota       do rotamer analysis?
*       chartGeom       do bond length and angle outliers?
*       chartCBdev      do CB dev plots and analysis?
*       chartBaseP      check base-phosphate perpendiculars?
*       chartSuite      check RNA backbone conformations?
*       chartHoriz      do horizontal chart?
*       chartCoot       do coot chart?
*       chartMulti      do html multi chart?
*       chartNotJustOut include residues that have no problems in the list?
*       chartAltloc     remove redundant residue rows when altlocs present?
*       chartImprove    compare to reduce -(no)build results to show improvement?
*
* This function returns some HTML suitable for using in a lab notebook entry.
*/
function runAnalysis($modelID, $opts)
{
    //{{{ Set up file/directory vars and the task list
    // If doKinemage or doCharts is off, turn off all their subordinates
    if (!$opts['doKinemage']) {
        foreach ($opts as $k => $v) {
            if (startsWith($k, 'kin')) {
                $opts[$k] = false;
            }
        }
    }
    if (!$opts['doCharts']) {
        foreach ($opts as $k => $v) {
            if (startsWith($k, 'chart')) {
                $opts[$k] = false;
            }
        }
    }
    if ($opts['kinForceViews']) {
        foreach ($opts as $k => $v) {
            if (startsWith($k, 'chart')) {
                $opts[$k] = true;
            }
        }
    }
    $model = $_SESSION['models'][$modelID];
    $modelDir = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
    $modelURL = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS;
    $kinDir = $_SESSION['dataDir'] . '/' . MP_DIR_KINS;
    $kinURL = $_SESSION['dataURL'] . '/' . MP_DIR_KINS;
    if (!file_exists($kinDir)) {
        mkdir($kinDir, 0777);
    }
    $rawDir = $_SESSION['dataDir'] . '/' . MP_DIR_RAWDATA;
    if (!file_exists($rawDir)) {
        mkdir($rawDir, 0777);
    }
    $chartDir = $_SESSION['dataDir'] . '/' . MP_DIR_CHARTS;
    $chartURL = $_SESSION['dataURL'] . '/' . MP_DIR_CHARTS;
    if (!file_exists($chartDir)) {
        mkdir($chartDir, 0777);
    }
    $xrayDir = $_SESSION['dataDir'] . '/' . MP_DIR_XRAYDATA;
    $infile = "{$modelDir}/{$model['pdb']}";
    $reduce_blength = $_SESSION['reduce_blength'];
    if (isset($model['mtz_file'])) {
        $mtz_file = $model['mtz_file'];
    } else {
        $mtz_file = $_SESSION['models'][$model['parent']]['mtz_file'];
    }
    if ($opts['chartRama']) {
        $tasks['rama'] = "Do Ramachandran analysis and make plots (<code>ramalyze</code>)";
    }
    if ($opts['chartRota']) {
        $tasks['rota'] = "Do rotamer analysis (<code>rotalyze</code>)";
    }
    if ($opts['chartCBdev']) {
        $tasks['cbeta'] = "Do C&beta; deviation analysis and make kins (<code>cbetadev</code>)";
    }
    if ($opts['chartOmega']) {
        $tasks['omega'] = "Do cis-peptide analysis (<code>omegalyze</code>)";
    }
    if ($opts['chartCablamLow']) {
        $tasks['cablam'] = "Do CaBLAM analysis (<code>cablam_validate</code>)";
    }
    if ($opts['chartBaseP']) {
        $tasks['base-phos'] = "Do RNA sugar pucker analysis";
    }
    if ($opts['chartSuite']) {
        $tasks['suitename'] = "Do RNA backbone conformations analysis";
    }
    if ($model['stats']['use_cdl']) {
        $geomsg = "Using CDL";
    } else {
        $geomsg = "";
    }
    if ($opts['chartGeom']) {
        $tasks['geomValidation'] = "Do bond length and angle geometry analysis (<code>mp_geo</code>) {$geomsg}";
    }
    if ($opts['chartClashlist']) {
        $tasks['clashlist'] = "Run <code>clashscore</code> to find bad clashes and clashscore";
    }
    if ($opts['chartImprove']) {
        $tasks['improve'] = "Suggest / report on fixes";
    }
    if ($opts['doCharts'] && !$opts['chartMulti']) {
        $tasks['chartsummary'] = "Create summary chart";
    }
    if ($opts['chartMulti']) {
        $tasks['multichart'] = "Create multi-criterion chart";
    }
    if ($opts['chartHoriz']) {
        $tasks['runRSCC'] = "Run real-space correlation";
        $tasks['charthoriz'] = "Create horizontal RSCC chart";
    }
    if ($opts['chartCoot']) {
        $tasks['cootchart'] = "Create chart for use in Coot";
    }
    if ($opts['doKinemage']) {
        $tasks['multikin'] = "Create multi-criterion kinemage";
    }
    //if($opts['doLowRes'])       $tasks['lowResKin'] = "Create low-resolution multi-criterion kinemage";
    //$doRem40 = $opts['chartClashlist'] || $opts['chartRama'] || $opts['chartRota'];
    //if($doRem40)                $tasks['remark40'] = "Create REMARK  40 record for the PDB file";
    //}}} Set up file/directory vars and the task list
    //{{{ Run geometry programs and offer kins to user
    //{{{ Ramachandran
    if ($opts['chartRama']) {
        $startTime = time();
        setProgress($tasks, 'rama');
        // updates the progress display if running as a background job
        $outfile = "{$rawDir}/{$model['prefix']}rama.data";
        runRamachandran($infile, $outfile);
        $rama = loadRamachandran($outfile);
        makeRamachandranKin($infile, "{$kinDir}/{$model['prefix']}rama.kin");
        $tasks['rama'] .= " - preview <a href='viewking.php?{$_SESSION['sessTag']}&url={$kinURL}/{$model['prefix']}rama.kin' target='_blank'>kinemage</a>";
        setProgress($tasks, 'rama');
        // so the preview link is visible
        makeRamachandranPDF($infile, "{$chartDir}/{$model['prefix']}rama.pdf");
        $tasks['rama'] .= " | <a href='{$chartURL}/{$model['prefix']}rama.pdf' target='_blank'>PDF</a>\n";
        setProgress($tasks, 'rama');
        // so the preview link is visible
        echo "Ramachandran ran for " . (time() - $startTime) . " seconds\n";
    }
    //}}}
    //{{{ Rotamers
    if ($opts['chartRota']) {
        $startTime = time();
        setProgress($tasks, 'rota');
        // updates the progress display if running as a background job
        $outfile = "{$rawDir}/{$model['prefix']}rota.data";
        runRotamer($infile, $outfile);
        $rota = loadRotamer($outfile);
        echo "Rotamers ran for " . (time() - $startTime) . " seconds\n";
    }
    //}}}
    //{{{ C-beta deviations
    if ($opts['chartCBdev']) {
        $startTime = time();
        setProgress($tasks, 'cbeta');
        // updates the progress display if running as a background job
        $outfile = "{$rawDir}/{$model['prefix']}cbdev.data";
        runCbetaDev($infile, $outfile);
        $cbdev = loadCbetaDev($outfile);
        makeCbetaDevPlot($infile, "{$kinDir}/{$model['prefix']}cbetadev.kin");
        $tasks['cbeta'] .= " - <a href='viewking.php?{$_SESSION['sessTag']}&url={$kinURL}/{$model['prefix']}cbetadev.kin' target='_blank'>preview</a>";
        setProgress($tasks, 'cbeta');
        // so the preview link is visible
        echo "C-beta ran for " . (time() - $startTime) . " seconds\n";
    }
    //}}}
    //{{{ Omega peptides
    if ($opts['chartOmega']) {
        $startTime = time();
        setProgress($tasks, 'omega');
        $outfile = "{$rawDir}/{$model['prefix']}omega.data";
        //$outfile = "$rawDir/$model[prefix]omega-clashlist.txt";
        runOmegalyze($infile, $outfile);
        $omega = loadOmegalyze($outfile);
        echo "Omegalyze ran for " . (time() - $startTime) . " seconds\n";
    }
    //}}}
    //{{{ CaBLAM
    if ($opts['chartCablamLow']) {
        setProgress($tasks, 'cablam');
        $outfile = "{$rawDir}/{$model['prefix']}cablam.data";
        runCablam($infile, $outfile);
        $cablam = loadCablam($outfile);
    }
    //}}}
    //{{{ Run nucleic acid geometry programs and offer kins to user
    //{{{ Base-phosphate perpendiculars
    if ($opts['chartBaseP']) {
        setProgress($tasks, 'base-phos');
        // updates the progress display if running as a background job
        $outfile = "{$rawDir}/{$model['prefix']}pperp.data";
        runBasePhosPerp($infile, $outfile);
        $pperp = loadBasePhosPerp($outfile);
    }
    //}}}
    //{{{ Suitename
    if ($opts['chartSuite']) {
        setProgress($tasks, 'suitename');
        // updates the progress display if running as a background job
        $outfile = "{$chartDir}/{$model['prefix']}suitename.txt";
        runSuitenameReport($infile, $outfile);
        $suites = loadSuitenameReport($outfile);
        $tasks['suitename'] .= " - <a href='viewtext.php?{$_SESSION['sessTag']}&file={$outfile}&mode=plain' target='_blank'>preview</a>\n";
        setProgress($tasks, 'suitename');
        // so the preview link is visible
        $outfile = "{$chartDir}/{$model['prefix']}suitestring.txt";
        runSuitenameString($infile, $outfile);
        makeSuitenameKin($infile, "{$kinDir}/{$model['prefix']}suitename.kin");
    }
    //}}}
    //}}} Run nucleic acid geometry programs and offer kins to user
    //{{{ Bonds and Angles
    if ($opts['chartGeom']) {
        setProgress($tasks, 'geomValidation');
        // updates the progress display if running as a background job
        $geomfile = "{$rawDir}/{$model['prefix']}geomvalidation.data";
        runValidationReport($infile, $geomfile, $model['stats']['use_cdl']);
        //$protfile = "$rawDir/$model[prefix]protvalidation.data";
        //runValidationReport($infile, $protfile, "protein");
        //$rnafile = "$rawDir/$model[prefix]rnavalidation.data";
        //runValidationReport($infile, $rnafile, "rna");
        //$validate_bond  = loadValidationBondReport($protfile,"protein");
        //if (is_array($validate_bond))
        $validate_bond = array_merge(loadValidationBondReport($geomfile, "protein"), loadValidationBondReport($geomfile, "rna"));
        if (count($validate_bond) == 0) {
            $validate_bond = null;
        }
        $validate_angle = array_merge(loadValidationAngleReport($geomfile, "protein"), loadValidationAngleReport($geomfile, "rna"));
        if (count($validate_angle) == 0) {
            $validate_angle = null;
        }
    }
    //}}}
    //}}} Run programs and offer kins to user
    //{{{ Run all-atom contact programs and offer kins to user
    // Clashes
    if ($opts['chartClashlist']) {
        $startTime = time();
        setProgress($tasks, 'clashlist');
        // updates the progress display if running as a background job
        $outfile = "{$chartDir}/{$model['prefix']}clashlist.txt";
        #runClashlist($infile, $outfile, $reduce_blength);
        runClashscore($infile, $outfile, $reduce_blength);
        #$clash = loadClashlist($outfile);
        $clash = loadClashscore($outfile);
        //$clashPct = runClashStats($model['stats']['resolution'], $clash['scoreAll'], $clash['scoreBlt40']);
        $tasks['clashlist'] .= " - <a href='viewtext.php?{$_SESSION['sessTag']}&file={$outfile}&mode=plain' target='_blank'>preview</a>\n";
        setProgress($tasks, 'clashlist');
        // so the preview link is visible
        echo "chartClashlist ran for " . (time() - $startTime) . " seconds\n";
    }
    //}}} Run all-atom contact programs and offer kins to user
    //{{{ Run real-space correlation
    $model['raw_rscc_name'] = "{$model['parent']}_raw.rscc";
    $model['rscc_name'] = "{$model['parent']}.rscc";
    $rscc_out = "{$xrayDir}/{$model['parent']}.rscc";
    $rscc_prequel_out = "{$xrayDir}/{$model['parent']}_prequel.rscc";
    if ($opts['chartHoriz']) {
        $startTime = time();
        setProgress($tasks, 'runRSCC');
        runRscc($infile, $mtz_file, $rscc_out, $rscc_prequel_out);
        echo "runRscc ran for " . (time() - $startTime) . " seconds\n";
        echo $mtz_file;
        echo isset($mtz_file);
    }
    //}}}
    //{{{ Report on improvements (that could be) made by MolProbity
    $improveText = "";
    if ($opts['chartImprove'] && ($clash || $rota)) {
        $startTime = time();
        setProgress($tasks, 'improve');
        // updates the progress display if running as a background job
        $altpdb = mpTempfile("tmp_altH_pdb_");
        $mainClashscore = $clash ? $clash['scoreAll'] : 0;
        $mainRotaCount = $rota ? count(findRotaOutliers($rota)) : 0;
        $improvementList = array();
        if ($model['isBuilt']) {
            $altInpath = $modelDir . '/' . $_SESSION['models'][$model['parent']]['pdb'];
            reduceNoBuild($altInpath, $altpdb, $reduce_blength);
            // Rotamers
            $outfile = mpTempfile("tmp_rotamer_");
            runRotamer($altpdb, $outfile);
            $altrota = loadRotamer($outfile);
            $altRotaCount = count(findRotaOutliers($altrota));
            if ($altRotaCount > $mainRotaCount) {
                if ($altRotaCount - $mainRotaCount > 1) {
                    $improvementList[] = "fixed " . ($altRotaCount - $mainRotaCount) . " bad rotamers";
                } else {
                    $improvementList[] = "fixed " . ($altRotaCount - $mainRotaCount) . " bad rotamer";
                }
            }
            unlink($outfile);
            // Clashes
            $outfile = mpTempfile("tmp_clashlist_");
            #runClashlist($altpdb, $outfile, $reduce_blength);
            runClashscore($altpdb, $outfile, $reduce_blength);
            #$altclash = loadClashlist($outfile);
            $altclash = loadClashscore($outfile);
            if ($altclash['scoreAll'] - $mainClashscore >= 0.005) {
                //0.005 is the smallest change that will still be reported by the sprintf("%.2f") below
                $improvementList[] = "improved your clashscore by " . sprintf("%.2f", $altclash['scoreAll'] - $mainClashscore) . " points";
            }
            unlink($outfile);
            if (count($improvementList) > 0) {
                $improveText .= "<div class='feature'>By adding H to this model and allowing Asn/Gln/His flips, you have already ";
                $improveText .= implode(" and ", $improvementList);
                $improveText .= ".  <br /><b>Make sure you download the modified PDB to take advantage of these improvements! <br />NOTE: Atom positions have changed, so refinement to idealize geometry is necessary.</b></div>\n";
            }
        } elseif ($mainClashscore > 0 || $mainRotaCount > 0) {
            if ($model['parent']) {
                $altInpath = $_SESSION['models'][$model['parent']]['pdb'];
            } else {
                $altInpath = $model['pdb'];
            }
            $altInpath = "{$modelDir}/{$altInpath}";
            reduceBuild($altInpath, $altpdb, $reduce_blength);
            if ($mainRotaCount > 0) {
                $outfile = mpTempfile("tmp_rotamer_");
                runRotamer($altpdb, $outfile);
                $altrota = loadRotamer($outfile);
                $altRotaCount = count(findRotaOutliers($altrota));
                if ($altRotaCount < $mainRotaCount) {
                    $improvementList[] = "fix " . ($mainRotaCount - $altRotaCount) . " bad rotamers";
                }
                unlink($outfile);
            }
            if ($mainClashscore > 0) {
                $outfile = mpTempfile("tmp_clashlist_");
                #runClashlist($altpdb, $outfile, $reduce_blength);
                runClashscore($altpdb, $outfile, $reduce_blength);
                #$altclash = loadClashlist($outfile);
                $altclash = loadClashscore($outfile);
                if ($mainClashscore - $altclash['scoreAll'] >= 0.005) {
                    //0.005 is the smallest change that will still be reported by the sprintf("%.2f") below
                    $improvementList[] = "improve your clashscore by " . sprintf("%.2f", $mainClashscore - $altclash['scoreAll']) . " points";
                }
                unlink($outfile);
            }
            if (count($improvementList) > 0) {
                $improveText .= "<div class='feature'>By adding H to this model and allowing Asn/Gln/His flips, we could <i>automatically</i> ";
                $improveText .= implode(" and ", $improvementList);
                $improveText .= ".</div>\n";
            }
        }
        unlink($altpdb);
        echo "chart Improve ran for " . (time() - $startTime) . " seconds\n";
    }
    //}}} Report on improvements (that could be) made by by MolProbity
    //{{{ Build multi-criterion chart, kinemage, horizontal, chart
    if ($opts['doCharts']) {
        $startTime = time();
        if ($opts['chartMulti']) {
            setProgress($tasks, 'multichart');
            // updates the progress display if running as a background job
        } else {
            setProgress($tasks, 'chartsummary');
        }
        $outfile = "{$rawDir}/{$model['prefix']}multi.table";
        $snapfile = "{$chartDir}/{$model['prefix']}multi.html";
        $resout = "{$rawDir}/{$model['prefix']}multi_res.table";
        writeMulticritChart($infile, $outfile, $snapfile, $resout, $clash, $rama, $rota, $cbdev, $pperp, $suites, $validate_bond, $validate_angle, $cablam, $omega, !$opts['chartNotJustOut'], $opts['chartMulti'], $opts['chartAltloc']);
        if ($opts['chartMulti']) {
            $tasks['multichart'] .= " - <a href='viewtable.php?{$_SESSION['sessTag']}&file={$outfile}' target='_blank'>preview</a>\n";
            setProgress($tasks, 'multichart');
            // so the preview link is visible
        } else {
            $tasks['chartsummary'] .= " - <a href='viewtable.php?{$_SESSION['sessTag']}&file={$outfile}' target='_blank'>preview</a>\n";
            setProgress($tasks, 'chartsummary');
            // so the preview link is visible
        }
        if ($opts['chartHoriz']) {
            setProgress($tasks, 'charthoriz');
            $horiz_table_file = "{$rawDir}/{$model['prefix']}horiz.table";
            writeHorizontalChart($resout, $rscc_out, $outfile, $horiz_table_file, $rscc_prequel_out);
        }
        if ($opts['chartCoot']) {
            setProgress($tasks, 'cootchart');
            $outfile = "{$chartDir}/{$model['prefix']}multi-coot.scm";
            $outfile_py = "{$chartDir}/{$model['prefix']}multi-coot.py";
            #makeCootMulticritChart($infile, $outfile, $clash, $rama, $rota, $cbdev, $pperp);
            makeCootClusteredChart($infile, $outfile, $outfile_py, $clash, $rama, $rota, $cbdev, $pperp);
        }
        echo "do Charts ran for " . (time() - $startTime) . " seconds\n";
    }
    if ($opts['doKinemage']) {
        $startTime = time();
        setProgress($tasks, 'multikin');
        // updates the progress display if running as a background job
        $mcKinOpts = array('ribbons' => $opts['kinRibbons'], 'Bscale' => $opts['kinBfactor'], 'Qscale' => $opts['kinOccupancy'], 'altconf' => $opts['kinAltConfs'], 'rama' => $opts['kinRama'], 'rota' => $opts['kinRota'], 'geom' => $opts['kinGeom'], 'cbdev' => $opts['kinCBdev'], 'omega' => $opts['kinOmega'], 'cablam' => $opts['kinCablamLow'], 'pperp' => $opts['kinBaseP'], 'clashdots' => $opts['kinClashes'], 'hbdots' => $opts['kinHbonds'], 'vdwdots' => $opts['kinContacts']);
        $outfile = "{$kinDir}/{$model['prefix']}multi.kin";
        $viewRes = array();
        //echo "kinForceViews = ".$opts['kinForceViews']."\n";
        if ($opts['kinForceViews']) {
            //echo "Ran calcLocalBadness\n";
            $viewRes = array_keys(calcLocalBadness($infile, 10, $clash, $rama, $rota, $cbdev, $pperp));
        }
        makeMulticritKin2(array($infile), $outfile, $mcKinOpts, $viewRes);
        // EXPERIMENTAL: gzip compress large multikins
        if (filesize($outfile) > MP_KIN_GZIP_THRESHOLD) {
            destructiveGZipFile($outfile);
        }
        echo "do Kinemage ran for " . (time() - $startTime) . " seconds\n";
    }
    //}}} Build multi-criterion chart, kinemage
    //{{{ Low-resolution-specific analyses
    //Low-res kinemage is being simplified and merged into main kinemage
    //if($opts['doLowRes'])
    //{
    //  if($opts['kinCablamLow'] || $opts['other'])
    //  {
    //      $startTime = time();
    //      setProgress($tasks, 'lowResKin');
    //      $lowResKinOpts = array(//first column is opts, second column sets true-false
    //          'ribbons'    =>  $opts['kinRibbons'],//pass pdb w/HELIX+SHEET for this
    //          'rama'       =>  $opts['kinRama'],
    //          'geom'       =>  $opts['kinGeom'],
    //          'cbdev'      =>  $opts['kinCBdev'],
    //          'omega'      =>  $opts['kinOmega'],
    //          'cablam'     =>  $opts['kinCablamLow'],
    //          'clashdots'  =>  $opts['kinClashes']
    //      );
    //      $outfile = "$kinDir/$model[prefix]low_multi.kin";
    //      $cablamSecStrucFile = "$modelDir/$model[prefix]cablam_sec_struc_records.pdb";
    //      //$viewRes = array(); //Used with opts[kinForceViews], not necessary argument for makeMulticritKin2
    //      makeMulticritKinLowRes(array($infile), $outfile, $cablamSecStrucFile, $lowResKinOpts);
    //      if(filesize($outfile) > MP_KIN_GZIP_THRESHOLD)  destructiveGZipFile($outfile);
    //      echo "do low-res Kinemage ran for ".(time() - $startTime)." seconds\n";
    //  }
    //}
    //}}}
    //{{{ Create REMARK  40 and insert into PDB file
    //if(is_array($clash) || is_array($rama) || is_array($rota))
    //{
    //    setProgress($tasks, 'remark40'); // updates the progress display if running as a background job
    //    $remark40 = makeRemark40($clash, $rama, $rota);
    //    replacePdbRemark($infile, $remark40,  40);
    //}
    //}}} Create REMARK  40 and insert into PDB file
    //{{{ Create lab notebook entry
    $entry = "";
    if (is_array($clash) || is_array($rama) || is_array($rota) || is_array($cbdev) || is_array($pperp) || is_array($suites)) {
        $entry .= "<h3>Summary statistics</h3>\n";
        $entry .= makeSummaryStatsTable($model['stats']['resolution'], $clash, $rama, $rota, $cbdev, $pperp, $suites, $validate_bond, $validate_angle, $cablam, $omega);
    }
    $entry .= $improveText;
    if ($opts['doKinemage'] || $opts['doCharts']) {
        $entry .= "<h3>Multi-criterion visualizations</h3>\n";
        $entry .= "<div class='indent'>\n";
        $entry .= "<table width='100%' border='0'><tr valign='top'>\n";
        if ($opts['doKinemage']) {
            $entry .= "<td>" . linkAnyFile("{$model['prefix']}multi.kin", "Kinemage", "img/multikin.jpg") . "</td>\n";
        }
        if ($opts['doCharts']) {
            $entry .= "<td>" . linkAnyFile("{$model['prefix']}multi.table", "Chart", "img/multichart.jpg") . "</td>\n";
            if ($opts['chartCoot']) {
                $entry .= "<td>" . linkAnyFile("{$model['prefix']}multi-coot.scm", "To-do list for Coot", "img/multichart-coot.jpg") . "<br><small><i>Open this in Coot 0.1.2 or later using Calculate | Run Script...</i></small></td>\n";
                #$entry .= "<td>".linkAnyFile("$model[prefix]multi-coot.py", "To-do list for Coot Python", "img/multichart-coot.jpg")."<br><small><i>Open this in Coot 0.1.2 or later using Calculate | Run Script...</i></small></td>\n";
            }
            if ($opts['chartHoriz']) {
                $entry .= "<td>" . linkAnyFile("{$model['prefix']}horiz.table", "Horizontal Chart", "img/multichart_horiz.jpg") . "</td>\n";
            }
        }
        //if($opts['doLowRes']) {
        //    if($opts['kinCablamLow'] || $opts['other']) {
        //        $entry .= "<td>".linkAnyFile("$model[prefix]low_multi.kin", "LowRes MultiKin", "img/low_multikin.jpg")."</td>\n";
        //    }
        //}
        $entry .= "</tr></table>\n";
        $entry .= "</div>\n";
    }
    if ($opts['chartClashlist'] || $opts['chartRama'] || $opts['chartCBdev'] || $opts['chartSuite']) {
        $entry .= "<h3>Single-criterion visualizations</h3>";
        $entry .= "<ul>\n";
        if ($opts['chartClashlist']) {
            $entry .= "<li>" . linkAnyFile("{$model['prefix']}clashlist.txt", "Clash list") . "</li>\n";
        }
        if ($opts['chartRama']) {
            $entry .= "<li>" . linkAnyFile("{$model['prefix']}rama.kin", "Ramachandran plot kinemage") . "</li>\n";
            $entry .= "<li>" . linkAnyFile("{$model['prefix']}rama.pdf", "Ramachandran plot PDF") . "</li>\n";
        }
        if ($opts['chartCBdev']) {
            $entry .= "<li>" . linkAnyFile("{$model['prefix']}cbetadev.kin", "C&beta; deviation scatter plot") . "</li>\n";
        }
        if ($opts['chartSuite']) {
            $entry .= "<li>" . linkAnyFile("{$model['prefix']}suitename.txt", "RNA backbone report") . "</li>\n";
            $entry .= "<li>" . linkAnyFile("{$model['prefix']}suitestring.txt", "RNA backbone conformation \"sequence\"") . "</li>\n";
            $entry .= "<li>" . linkAnyFile("{$model['prefix']}suitename.kin", "RNA backbone multi-D plot of conformations") . "</li>\n";
        }
        $entry .= "</ul>\n";
    }
    if ($remark40) {
        $entry .= "<h3>REMARK  40</h3>";
        $url = "{$modelURL}/{$model['pdb']}";
        $entry .= "You can <a href='{$url}'>download your PDB file with REMARK  40</a> inserted, or the same <a href='download_trimmed.php?{$_SESSION['sessTag']}&file={$infile}'> without hydrogens</a>.\n";
        $entry .= "<p><pre>{$remark40}</pre></p>";
    }
    //}}} Create lab notebook entry
    setProgress($tasks, null);
    // everything is finished
    return $entry;
}