I use Jmol embedded within a custom Java application.
I’m deleting some bonds then atoms by running a command like this:
JmolViewer viewer; // Gets defined.// ...
String script = "connect (Rh1) (B155) delete;connect (Rh1) (B93)
delete;connect (B155) (Rh1) delete;connect (B155) (B101)
delete;connect (B155) (C3) delete;connect (B155) (B140) delete;connect
(B155) (B154) delete;connect (B155) (B159) delete;connect (B155)
(B156) delete;connect (B155) (B33) delete;connect (B155) (B45)
delete;connect (C2) (B159) delete;connect (C2) (C1) delete;connect
(C3) (S2) delete;connect (C3) (S3) delete;connect (C3) (C1)
delete;connect (C3) (B159) delete;connect (C3) (B157) delete;connect
(C3) (B156) delete;connect (C3) (B155) delete;connect (C3) (B154)
delete;connect (C3) (B140) delete;connect (C3) (B135) delete;connect
(C3) (B133) delete;connect (C3) (B45) delete;connect (B33) (S3)
delete;connect (B33) (B155) delete;connect (B33) (B38) delete;connect
(B45) (S3) delete;connect (B45) (S4) delete;connect (B45) (C3)
delete;connect (B45) (B159) delete;connect (B45) (B157) delete;connect
(B45) (B155) delete;connect (B45) (B154) delete;connect (B45) (B140)
delete;connect (B45) (B135) delete;connect (B45) (B133) delete;connect
(B45) (B101) delete;connect (B101) (S2) delete;connect (B101) (S3)
delete;connect (B101) (B159) delete;connect (B101) (B157)
delete;connect (B101) (B156) delete;connect (B101) (B155)
delete;connect (B101) (B140) delete;connect (B101) (B135)
delete;connect (B101) (B133) delete;connect (B101) (C1) delete;connect
(B101) (B45) delete;connect (B101) (B85) delete;connect (B133) (S4)
delete;connect (B133) (S5) delete;connect (B133) (B101) delete;connect
(B133) (C3) delete;connect (B133) (B159) delete;connect (B133) (B157)
delete;connect (B133) (B156) delete;connect (B133) (B154)
delete;connect (B133) (B135) delete;connect (B133) (B45)
delete;connect (B135) (S3) delete;connect (B135) (S4) delete;connect
(B135) (B101) delete;connect (B135) (C1) delete;connect (B135) (C3)
delete;connect (B135) (B133) delete;connect (B135) (B159)
delete;connect (B135) (B157) delete;connect (B135) (B156)
delete;connect (B135) (B154) delete;connect (B135) (B140)
delete;connect (B135) (B45) delete;connect (B140) (S4) delete;connect
(B140) (S5) delete;connect (B140) (B101) delete;connect (B140) (C3)
delete;connect (B140) (B159) delete;connect (B140) (B157)
delete;connect (B140) (B156) delete;connect (B140) (B155)
delete;connect (B140) (B154) delete;connect (B140) (B135)
delete;connect (B140) (B45) delete;connect (B154) (S2) delete;connect
(B154) (S5) delete;connect (B154) (C1) delete;connect (B154) (C3)
delete;connect (B154) (B140) delete;connect (B154) (B133)
delete;connect (B154) (B135) delete;connect (B154) (B157)
delete;connect (B154) (B156) delete;connect (B154) (B155)
delete;connect (B154) (B45) delete;connect (B154) (B93) delete;connect
(B156) (S2) delete;connect (B156) (S5) delete;connect (B156) (B101)
delete;connect (B156) (C3) delete;connect (B156) (B140) delete;connect
(B156) (B133) delete;connect (B156) (B135) delete;connect (B156)
(B159) delete;connect (B156) (B157) delete;connect (B156) (B154)
delete;connect (B156) (B155) delete;connect (B157) (S4) delete;connect
(B157) (S5) delete;connect (B157) (B101) delete;connect (B157) (C1)
delete;connect (B157) (C3) delete;connect (B157) (B140) delete;connect
(B157) (B133) delete;connect (B157) (B135) delete;connect (B157)
(B156) delete;connect (B157) (B154) delete;connect (B157) (B45)
delete;connect (B159) (S4) delete;connect (B159) (B101) delete;connect
(B159) (C2) delete;connect (B159) (C1) delete;connect (B159) (C3)
delete;connect (B159) (B140) delete;connect (B159) (B133)
delete;connect (B159) (B135) delete;connect (B159) (B156)
delete;connect (B159) (B155) delete;connect (B159) (B45)
delete;connect (Rh2) (B87) delete;connect (C4) (B158) delete;connect
(C4) (B4) delete;connect (B15) (S1) delete;connect (B15) (P3)
delete;connect (B15) (B4) delete;connect (B15) (B160) delete;connect
(B15) (B158) delete;connect (B15) (B152) delete;connect (B15) (B137)
delete;connect (B15) (B73) delete;connect (B73) (P1) delete;connect
(B73) (P5) delete;connect (B73) (B15) delete;connect (B73) (B158)
delete;connect (B73) (B152) delete;connect (B73) (B137) delete;connect
(B137) (P1) delete;connect (B137) (P3) delete;connect (B137) (B4)
delete;connect (B137) (B160) delete;connect (B137) (B158)
delete;connect (B137) (B152) delete;connect (B137) (B15)
delete;connect (B137) (B73) delete;connect (B152) (S1) delete;connect
(B152) (P5) delete;connect (B152) (B137) delete;connect (B152) (B15)
delete;connect (B152) (B158) delete;connect (B152) (B73)
delete;connect (B158) (P1) delete;connect (B158) (C4) delete;connect
(B158) (B4) delete;connect (B158) (B137) delete;connect (B158) (B15)
delete;connect (B158) (B160) delete;connect (B158) (B152)
delete;connect (B158) (B73) delete;connect (B158) (B87) delete;connect
(B160) (S1) delete;connect (B160) (P1) delete;connect (B160) (P5)
delete;connect (B160) (B137) delete;connect (B160) (B15)
delete;connect (B160) (B158) delete;delete B155;delete C2;delete
C3;delete B33;delete B45;delete B101;delete B133;delete B135;delete
B140;delete B154;delete B156;delete B157;delete B159;delete C4;delete
B15;delete B73;delete B137;delete B152;delete B158;delete B160;"
viewer.scriptWaitStatus(script, null);
// I've also tried this:
viewer.getProperty(null, "evaluate", "script(' "+script+ "; refresh ')");
After this has run I inspect the first viewer model:
final short nAtoms = (short) viewer.getAtomCountInModel(0);for (short
id = 0; id < nAtoms; ++id) {
org.jmol.modelset.Atom atom = (org.jmol.modelset.Atom)
viewer.getAtomPoint3f(id);
System.out.println(atom.getAtomName());
}
The atoms I’ve deleted are listed as still in the model. Why?
If I try to manipulate these deleted atoms in the Jmol console, the output
suggests they don’t exist.
How can I get the viewer model to update so the atoms really are deleted?
Cheers,
Dave
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