public static void main(String[] args) {
try {
Structure struc = StructureIO.getStructure("1aoi");
StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();
jmolPanel.setStructure(struc);
// send some RASMOL style commands to Jmol
jmolPanel.evalString("select * ; color chain;");
jmolPanel.evalString("select nucleic; cartoon on;");
jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on; ");
} catch (Exception e) {
e.printStackTrace();
}
}
private void updateJmolDisplay() {
if (jmol == null) return;
int size = afpChain.getAlnLength();
StringBuffer cmd = new StringBuffer("select ");
int nrSelected = 0;
try {
for (int i = 0; i < size; i++) {
if (selection.get(i)) {
Atom a1 = DisplayAFP.getAtomForAligPos(afpChain, 0, i, ca1, false);
Atom a2 = DisplayAFP.getAtomForAligPos(afpChain, 1, i, ca2, false);
String select1 = "";
if (a1 != null) select1 = JmolTools.getPdbInfo(a1);
String select2 = "";
if (a2 != null) select2 = JmolTools.getPdbInfo(a2);
// nothing to display
if (select1.equals("") && select2.equals("")) continue;
if (nrSelected > 0) cmd.append(", ");
cmd.append(select1);
cmd.append(", ");
cmd.append(select2);
nrSelected++;
}
}
} catch (StructureException e) {
e.printStackTrace();
}
if (nrSelected == 0) cmd.append(" none;");
else cmd.append("; set display selected;");
jmol.evalString(cmd.toString());
}