src/hg/hgc/virusClick.c 1.6
1.6 2009/06/15 23:00:24 markd
highlight only specific sequence differences in gene seq display
Index: src/hg/hgc/virusClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/virusClick.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/hgc/virusClick.c 15 Jun 2009 21:48:03 -0000 1.5
+++ src/hg/hgc/virusClick.c 15 Jun 2009 23:00:24 -0000 1.6
@@ -1,593 +1,602 @@
/* virusClick - hgc code for a prototype virus browser on the h1n1 genome */
#include "common.h"
#include "hgc.h"
#include "virusClick.h"
#include "hCommon.h"
#include "linefile.h"
#include "dystring.h"
#include "lsSnpPdbChimera.h"
#include "jksql.h"
#include "net.h"
#include "trashDir.h"
#include "htmshell.h"
static void h1n1DownloadPdb(char *item, char *pdbUrl, struct tempName *tmpPdb)
/* uncompress PDB to trash */
{
int inFd = netOpenHttpExt(pdbUrl, "GET", TRUE);
int inFdRedir = 0;
char *pdbUrlRedir = NULL;
if (!netSkipHttpHeaderLinesHandlingRedirect(inFd, pdbUrl, &inFdRedir, &pdbUrlRedir))
errAbort("Unable to access predicted 3D structure file: %s", pdbUrl);
if (pdbUrlRedir != NULL)
{
close(inFd);
inFd = inFdRedir;
freez(&pdbUrlRedir);
}
trashDirFile(tmpPdb, "hgct", item, ".pdb");
FILE *outFh = mustOpen(tmpPdb->forCgi, "w");
struct lineFile *inLf = lineFileDecompressFd(pdbUrl, TRUE, inFd);
char *line;
while (lineFileNext(inLf, &line, NULL))
{
fputs(line, outFh);
fputc('\n', outFh);
}
lineFileClose(&inLf);
carefulClose(&outFh);
}
static void h1n1MkChimeraxTrashFullUrl(struct tempName *tmpPdb, char *fullUrl, int fullUrlSize)
/* generate full URL for a chimerax file decompressed to trash */
{
// FIXME: this is not generate (URL generation will not work on all web servers).
// if this is kept, should address this.
char *serverName = getenv("SERVER_NAME");
char *serverPort = getenv("SERVER_PORT");
char *scriptName = getenv("SCRIPT_NAME");
if ((serverName != NULL) && (serverPort != NULL) && (scriptName != NULL))
{
// remote url
safef(fullUrl, fullUrlSize, "http://%s", serverName);
if (!sameString(serverPort, "80"))
{
safecat(fullUrl, fullUrlSize, ":");
safecat(fullUrl, fullUrlSize, serverPort);
}
safecat(fullUrl, fullUrlSize, scriptName);
char *p = strrchr(fullUrl, '/');
if (p != NULL)
*++p = '\0'; // drop cgi name, keeping directory
safecat(fullUrl, fullUrlSize, tmpPdb->forHtml);
}
else
{
// local url
safef(fullUrl, fullUrlSize, "file:///%s/%s", getCurrentDir(), tmpPdb->forHtml);
}
}
static char *mkChimeraPyScript(char *scriptFile)
/* create chimera python script from commands in scriptFile */
{
struct dyString *buf = dyStringNew(0);
dyStringAppend(buf, "from chimera import runCommand\n");
struct lineFile *lf = lineFileOpen(scriptFile, TRUE);
char *line;
while (lineFileNextReal(lf, &line))
dyStringPrintf(buf, "runCommand(\"%s\")\n", line);
lineFileClose(&lf);
return dyStringCannibalize(&buf);
}
static void mkChimerax(char *item, char *pdbUrl, char *scriptFile, struct tempName *chimerax)
/* generate a chimerax file for downloading h1n1 PDB structure */
{
// chimera doesn't handle compressed files via URL, so uncompress into the trash
struct tempName tmpPdb;
char usePdbUrl[PATH_LEN];
if (endsWith(pdbUrl, ".gz") || endsWith(pdbUrl, ".Z"))
{
h1n1DownloadPdb(item, pdbUrl, &tmpPdb);
h1n1MkChimeraxTrashFullUrl(&tmpPdb, usePdbUrl, sizeof(usePdbUrl));
}
else
safecpy(usePdbUrl, sizeof(usePdbUrl), pdbUrl);
char *pyScript = NULL;
if (scriptFile != NULL)
pyScript = mkChimeraPyScript(scriptFile);
lsSnpPdbChimeraGenericLink(usePdbUrl, pyScript, "hgct", item, chimerax);
freeMem(pyScript);
}
static void tempNameFromPrefix(struct tempName *name, struct tempName *prefix, char *suffix)
/* build a tempName based on an existing tempName and a suffix */
{
safecpy(name->forCgi, sizeof(name->forCgi), prefix->forCgi);
safecat(name->forCgi, sizeof(name->forCgi), suffix);
safecpy(name->forHtml, sizeof(name->forHtml), prefix->forHtml);
safecat(name->forHtml, sizeof(name->forHtml), suffix);
}
/* location and url of h1n1 modeling directory */
static char *h1n1StructDir = "/projects/compbio/experiments/protein-predict/h1n1";
static char *h1n1StructUrl = "http://users.soe.ucsc.edu/~karplus/h1n1";
static boolean getH1n1Model(char *gene, char *pdbUrl)
/* Find model PDB file URL, return false if does not exist. URL is
* return in pdbUrl if it is not NULL */
{
char relPath[PATH_LEN], pdbPath[PATH_LEN];
if (sameString(gene, "HA"))
safef(relPath, sizeof(relPath), "%s/%s", gene, "consensus.uncleaved.D18-G519.pdb");
else if (sameString(gene, "NA"))
safef(relPath, sizeof(relPath), "%s/%s", gene, "consensus.tetramer.V83-I467.pdb");
else
return FALSE;
if (pdbUrl != NULL)
safef(pdbUrl, PATH_LEN, "%s/%s", h1n1StructUrl, relPath);
safef(pdbPath, sizeof(pdbPath), "%s/%s", h1n1StructDir, relPath);
return fileExists(pdbPath);
}
-static void mkH1n1StructData(char *gene, char *idPairFile,
+static void mkH1n1StructData(char *gene, char *idPairFile, char *highlightId,
struct tempName *imageFile, struct tempName *chimeraScript)
-/* generate 3D structure files; idPairFile can be NULL */
+/* generate 3D structure files; difference highlighting is generate only idPairFile or
+ * idPairFile, if specified, but not both. */
{
struct tempName prefix;
trashDirFile(&prefix, "hgct", gene, "tmp");
char idFile[PATH_LEN], idArg[PATH_LEN], logFile[PATH_LEN], cmd[2*PATH_LEN];
idArg[0] = '\0';
-if (idPairFile != NULL)
+if ((idPairFile != NULL) || (highlightId != NULL))
+ {
+ safef(idFile, sizeof(idFile), "%s.ids", prefix.forCgi);
+ if (idPairFile != NULL)
{
// extract first column
- safef(idFile, sizeof(idFile), "%s.ids", idPairFile);
safef(cmd, sizeof(cmd), "cut -f 1 %s >%s", idPairFile, idFile);
if (system(cmd) != 0)
errAbort("extracting protein ids failed: %s", cmd);
+ }
+ else
+ {
+ FILE *fh = mustOpen(idFile, "w");
+ fprintf(fh, "%s\n", highlightId);
+ carefulClose(&fh);
+ }
safef(idArg, sizeof(idArg), "--ids %s", idFile);
}
// dynamic_highlight.pl knows locations of model files
safef(logFile, sizeof(logFile), "%s.log", prefix.forCgi);
safef(cmd, sizeof(cmd), "%s/dynamic_highlight.pl --rasmol --chimera --protein %s --consensus 0602 %s --base %s >%s 2>&1",
h1n1StructDir, gene, idArg, prefix.forCgi, logFile);
if (system(cmd) != 0)
errAbort("creation of 3D structure highlight files failed: %s", cmd);
// output names are all predefined by script relative to prefix
tempNameFromPrefix(imageFile, &prefix, "_highlight.jpg");
tempNameFromPrefix(chimeraScript, &prefix, "_highlight.cmd");
}
static void showProtH1n1(char *item, char *geneSymbol)
{
char query2[256];
struct sqlResult *sr2;
char **row2;
struct sqlConnection *conn2 = hAllocConn(database);
char *subjId, *dnaSeqId;
char *aaSeqId= NULL;
char *gene=NULL;
char cond_str[256];
char *predFN;
char *homologID;
char *SCOPdomain;
char *chain;
char goodSCOPdomain[40];
int first = 1;
float eValue;
char *chp;
int homologCount;
int gotPDBFile = 0;
safef(query2, sizeof(query2),
"select subjId, dnaSeqId, aaSeqId, gene from gisaidXref where dnaSeqId='%s'", item);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
if (row2 != NULL)
{
subjId = strdup(row2[0]);
dnaSeqId = strdup(row2[1]);
aaSeqId = strdup(row2[2]);
gene = strdup(row2[3]);
}
else
{
errAbort("%s not found.", item);
}
sqlFreeResult(&sr2);
printf("<H3>Protein Structure Analysis and Prediction</H3>");
printf("<B>Comparison to 1918 Flu Virus:</B> ");
printf("<A HREF=\"%s/%s/%s/1918_%s.mutate", h1n1StructUrl, gene, aaSeqId, aaSeqId);
printf("\" TARGET=_blank>%s</A><BR>\n", aaSeqId);
printf("<B>Comparison to A H1N1 gene %s concensus:</B> ", gene);
printf("<A HREF=\"%s/%s/%s/consensus_%s.mutate", h1n1StructUrl, gene, aaSeqId, aaSeqId);
printf("\" TARGET=_blank>%s</A><BR>\n", aaSeqId);
printf("<BR><B>3D Structure Prediction of %s concensus sequence (with variation of sequence %s highlighted):", geneSymbol, item);
printf("<BR>PDB file:</B> ");
char pdbUrl[PATH_LEN];
safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", h1n1StructUrl, item, item);
// Modeller stuff
char modelPdbUrl[PATH_LEN];
if (getH1n1Model(gene, modelPdbUrl))
{
- char *selectFile = cartOptionalString(cart, gisaidAaSeqList);
struct tempName imageFile, chimeraScript, chimerax;
- mkH1n1StructData(gene, selectFile, &imageFile, &chimeraScript);
+ mkH1n1StructData(gene, NULL, aaSeqId, &imageFile, &chimeraScript);
mkChimerax(gene, modelPdbUrl, chimeraScript.forCgi, &chimerax);
printf("<A HREF=\"%s\" TARGET=_blank>%s</A>, view with <A HREF=\"%s\">Chimera</A><BR>\n", modelPdbUrl, gene, chimerax.forHtml);
printf("<TABLE>\n");
printf("<TR>\n");
printf("<TD ALIGN=\"center\"><img src=\"%s\"></TD>", imageFile.forHtml);
printf("</TR>\n");
printf("</TABLE>\n");
}
return;
gotPDBFile = 0;
safef(cond_str, sizeof(cond_str), "proteinID='%s' and evalue <1.0e-5;", item);
printf("<TABLE>\n");
printf("<TR><TD ALIGN=\"center\">Front</TD>\n");
printf("<TD ALIGN=\"center\">Top</TD>\n");
printf("<TD ALIGN=\"center\">Side</TD>\n");
printf("</TR>\n");
printf("<TR>\n");
printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view1_200.jpg\"></TD>", h1n1StructUrl, item, item);
printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view2_200.jpg\"></TD>", h1n1StructUrl, item, item);
printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view3_200.jpg\"></TD>", h1n1StructUrl, item, item);
printf("</TR>\n");
printf("<TR>\n");
printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view1_500.jpg\">500x500</A></TD>",
h1n1StructUrl, item, item);
printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view2_500.jpg\">500x500</A></TD>",
h1n1StructUrl, item, item);
printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view3_500.jpg\">500x500</A></TD>",
h1n1StructUrl, item, item);
printf("</TR>\n");
printf("</TABLE>\n");
printf("<BR><B>Detailed results of SAM-T02:</B> ");
printf("<A HREF=\"%s/%s/summary.html", h1n1StructUrl, item);
printf("\" TARGET=_blank>%s</A><BR>\n", item);
/* by pass the following additional processing for now, until two necessary tables are built */
hFreeConn(&conn2);
return;
if (sqlGetField(database, "protHomolog", "proteinID", cond_str) != NULL)
{
safef(cond_str, sizeof(cond_str), "proteinID='%s'", item);
predFN = sqlGetField(database, "protPredFile", "predFileName", cond_str);
if (predFN != NULL)
{
printf("<A HREF=\"../SARS/%s/", item);
/* printf("%s.t2k.undertaker-align.pdb\">%s</A><BR>\n", item,item); */
printf("%s\">%s</A><BR>\n", predFN,item);
gotPDBFile = 1;
}
}
if (!gotPDBFile)
{
printf("No high confidence level structure prediction available for this sequence.");
printf("<BR>\n");
}
printf("<B>3D Structure of Close Homologs:</B> ");
homologCount = 0;
strcpy(goodSCOPdomain, "dummy");
conn2= hAllocConn(database);
safef(query2, sizeof(query2),
"select homologID,eValue,SCOPdomain,chain from sc1.protHomolog where proteinID='%s' and evalue <= 0.01;",
item);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
if (row2 != NULL)
{
while (row2 != NULL)
{
homologID = row2[0];
sscanf(row2[1], "%e", &eValue);
SCOPdomain = row2[2];
chp = SCOPdomain+strlen(SCOPdomain)-1;
while (*chp != '.') chp--;
*chp = '\0';
chain = row2[3];
if (eValue <= 1.0e-10)
strcpy(goodSCOPdomain, SCOPdomain);
else
{
if (strcmp(goodSCOPdomain,SCOPdomain) != 0)
goto skip;
else
if (eValue > 0.1) goto skip;
}
if (first)
first = 0;
else
printf(", ");
printf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphics&pdbId=%s",
homologID);
if (strlen(chain) >= 1)
printf("\"TARGET=_blank>%s(chain %s)</A>", homologID, chain);
else
printf("\"TARGET=_blank>%s</A>", homologID);
homologCount++;
skip:
row2 = sqlNextRow(sr2);
}
}
hFreeConn(&conn2);
sqlFreeResult(&sr2);
if (homologCount == 0)
printf("None<BR>\n");
printf("<BR><B>Details:</B> ");
printf("<A HREF=\"../SARS/%s/summary.html", item);
printf("\" TARGET=_blank>%s</A><BR>\n", item);
htmlHorizontalLine();
}
void showSAM_h1n1(char *item)
{
char query2[256];
struct sqlResult *sr2;
char **row2;
struct sqlConnection *conn2 = hAllocConn(database);
char cond_str[256];
char *predFN;
char *homologID;
char *SCOPdomain;
char *chain;
char goodSCOPdomain[40];
int first = 1;
float eValue;
char *chp;
int homologCount;
int gotPDBFile = 0;
printf("<H3>Protein Structure Analysis and Prediction by ");
printf("<A HREF=\"http://www.soe.ucsc.edu/research/compbio/SAM_T02/sam-t02-faq.html\"");
printf(" TARGET=_blank>SAM-T02</A></H3>\n");
printf("<B>Multiple Alignment:</B> ");
printf("<A HREF=\"%s/%s/summary.html#alignment", h1n1StructUrl, item);
printf("\" TARGET=_blank>%s</A><BR>\n", item);
printf("<B>Secondary Structure Predictions:</B> ");
printf("<A HREF=\"%s/%s/summary.html#secondary-structure", h1n1StructUrl, item);
printf("\" TARGET=_blank>%s</A><BR>\n", item);
printf("<B>3D Structure Prediction (PDB file):</B> ");
char pdbUrl[PATH_LEN];
safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", h1n1StructUrl, item, item);
struct tempName chimerax;
mkChimerax(item, pdbUrl, NULL, &chimerax);
printf("<A HREF=\"%s\" TARGET=_blank>%s</A>, view with <A HREF=\"%s\">Chimera</A><BR>\n", pdbUrl, item, chimerax.forHtml);
gotPDBFile = 0;
safef(cond_str, sizeof(cond_str), "proteinID='%s' and evalue <1.0e-5;", item);
printf("<TABLE>\n");
printf("<TR><TD ALIGN=\"center\">Front</TD>\n");
printf("<TD ALIGN=\"center\">Top</TD>\n");
printf("<TD ALIGN=\"center\">Side</TD>\n");
printf("</TR>\n");
printf("<TR>\n");
printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view1_200.jpg\"></TD>", h1n1StructUrl, item, item);
printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view2_200.jpg\"></TD>", h1n1StructUrl, item, item);
printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view3_200.jpg\"></TD>", h1n1StructUrl, item, item);
printf("</TR>\n");
printf("<TR>\n");
printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view1_500.jpg\">500x500</A></TD>",
h1n1StructUrl, item, item);
printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view2_500.jpg\">500x500</A></TD>",
h1n1StructUrl, item, item);
printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view3_500.jpg\">500x500</A></TD>",
h1n1StructUrl, item, item);
printf("</TR>\n");
printf("</TABLE>\n");
printf("<BR><B>Detailed results of SAM-T02:</B> ");
printf("<A HREF=\"%s/%s/summary.html", h1n1StructUrl, item);
printf("\" TARGET=_blank>%s</A><BR>\n", item);
/* by pass the following additional processing for now, until two necessary tables are built */
hFreeConn(&conn2);
return;
if (sqlGetField(database, "protHomolog", "proteinID", cond_str) != NULL)
{
safef(cond_str, sizeof(cond_str), "proteinID='%s'", item);
predFN = sqlGetField(database, "protPredFile", "predFileName", cond_str);
if (predFN != NULL)
{
printf("<A HREF=\"../SARS/%s/", item);
/* printf("%s.t2k.undertaker-align.pdb\">%s</A><BR>\n", item,item); */
printf("%s\">%s</A><BR>\n", predFN,item);
gotPDBFile = 1;
}
}
if (!gotPDBFile)
{
printf("No high confidence level structure prediction available for this sequence.");
printf("<BR>\n");
}
printf("<B>3D Structure of Close Homologs:</B> ");
homologCount = 0;
strcpy(goodSCOPdomain, "dummy");
conn2= hAllocConn(database);
safef(query2, sizeof(query2),
"select homologID,eValue,SCOPdomain,chain from sc1.protHomolog where proteinID='%s' and evalue <= 0.01;",
item);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
if (row2 != NULL)
{
while (row2 != NULL)
{
homologID = row2[0];
sscanf(row2[1], "%e", &eValue);
SCOPdomain = row2[2];
chp = SCOPdomain+strlen(SCOPdomain)-1;
while (*chp != '.') chp--;
*chp = '\0';
chain = row2[3];
if (eValue <= 1.0e-10)
strcpy(goodSCOPdomain, SCOPdomain);
else
{
if (strcmp(goodSCOPdomain,SCOPdomain) != 0)
goto skip;
else
if (eValue > 0.1) goto skip;
}
if (first)
first = 0;
else
printf(", ");
printf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphics&pdbId=%s",
homologID);
if (strlen(chain) >= 1)
printf("\"TARGET=_blank>%s(chain %s)</A>", homologID, chain);
else
printf("\"TARGET=_blank>%s</A>", homologID);
homologCount++;
skip:
row2 = sqlNextRow(sr2);
}
}
hFreeConn(&conn2);
sqlFreeResult(&sr2);
if (homologCount == 0)
printf("None<BR>\n");
printf("<BR><B>Details:</B> ");
printf("<A HREF=\"../SARS/%s/summary.html", item);
printf("\" TARGET=_blank>%s</A><BR>\n", item);
htmlHorizontalLine();
}
void doH1n1Seq(struct trackDb *tdb, char *item)
/* Show extra info for H1N1 Seq Annotations track. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char query[256];
char **row;
char *geneSymbol=NULL;
genericHeader(tdb, item);
/*pslList = getAlignments(conn, track, item);
printAlignmentsSimple(pslList, start, "h1n1Seq", track, item);
*/
sprintf(query, "select seqId, geneSymbol, strain, islId from h1n1SeqXref where seqId = '%s'", item);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
char *seqId, *strain, *islId;
seqId = row[0];
geneSymbol = row[1];
strain = row[2];
islId = row[3];
printf("<B>Sequence ID: %s</B> <BR>", seqId);
printf("<B>Gene: %s</B> <BR>", geneSymbol);
printf("<B>Strain: %s</B> <BR>", strain);
printf("<B>Isolate: </B> ");
printf("<A HREF=\"../cgi-bin/gisaidSample?hgs_sample=%s&submit=Go\">%s</A>",
islId, islId);
}
htmlHorizontalLine();
//showSAM_h1n1(item);
showProtH1n1(item, geneSymbol);
htmlHorizontalLine();
printTrackHtml(tdb);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
void doH1n1Gene(struct trackDb *tdb, char *item)
/* Show details page for H1N1 Genes and Regions annotations track. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char query[256];
char **row;
char *chrom, *chromStart, *chromEnd;
char *gene=NULL;
genericHeader(tdb, item);
gene = item;
printf("<B>Gene: </B> %s\n<BR>", gene);
sprintf(query, "select chrom, chromStart, chromEnd from h1n1Gene where name='%s';", gene);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
chrom = row[0];
chromStart = row[1];
chromEnd = row[2];
printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, item);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
htmlHorizontalLine();
printf("<H3>Protein Structure Analysis and Prediction</H3>");
printf("<B>3D Structure Prediction of consensus sequence (with variations of all selected sequences highlighted):");
printf("<BR>PDB file:</B> ");
char pdbUrl[PATH_LEN];
safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", h1n1StructUrl, item, item);
// Modeller stuff
char modelPdbUrl[PATH_LEN];
if (getH1n1Model(gene, modelPdbUrl))
{
char *selectFile = cartOptionalString(cart, gisaidAaSeqList);
struct tempName imageFile, chimeraScript, chimerax;
- mkH1n1StructData(gene, selectFile, &imageFile, &chimeraScript);
+ mkH1n1StructData(gene, selectFile, NULL, &imageFile, &chimeraScript);
mkChimerax(gene, modelPdbUrl, chimeraScript.forCgi, &chimerax);
printf("<A HREF=\"%s\" TARGET=_blank>%s</A>, view with <A HREF=\"%s\">Chimera</A><BR>\n",
modelPdbUrl, gene, chimerax.forHtml);
printf("<TABLE>\n");
printf("<TR>\n");
printf("<TD ALIGN=\"center\"><img src=\"%s\"></TD>", imageFile.forHtml);
printf("</TR>\n");
printf("</TABLE>\n");
}
htmlHorizontalLine();
printTrackHtml(tdb);
sqlFreeResult(&sr);
hFreeConn(&conn);
}