It's a flaw in the select for water, which includes
oxygen & connected(2, hydrogen or deuterium or tritium), (hydrogen or
deuterium or tritium) & connected(oxygen & connected(2, hydrogen or
deuterium or tritium))
In this model there are "H2O" fragments within the protein, though I agree
that's not "water"
water and not protein
is a workaround.
I'll fix that in Jmol 11.9.7 and 11.8.8.
Bob
On Wed, Oct 28, 2009 at 10:09 AM, Charles Shubert <cshub...@mit.edu> wrote:
> It seems to me that there is a small problem with parsing pdb files
> that contain hydrogen atoms. I don't see this problem with most pdb
> files.
>
> --Chuck
>
> Using 1GXX this code snippet produces the output below:
>
> private String[] getMoleculeElements(String script)
> {
> if(null != script)
> {
> System.out.println("\nViewer.getMoleculeElements
> script: " + script);
> MySelectionListener mySelectionListener = new
> MySelectionListener();
>
> getJmolViewer().addSelectionListener(mySelectionListener);
>
> getJmolViewer().scriptWait(script);
>
> int atomCount = getJmolViewer().getSelectionCount();
> BitSet bitSet =
> mySelectionListener.getSelectionBitSet();
>
>
> getJmolViewer().removeSelectionListener(mySelectionListener);
>
> return extractArray(atomCount, bitSet);
> }
> return null;
> }
>
> public String[] extractArray(int count, BitSet bitset)
> {
> ArrayList<String> arrayList = new ArrayList<String>();
> String current = null;
> int bitIndex = 0;
> for(int i=0; count != i; i++)
> {
> bitIndex = bitset.nextSetBit(bitIndex);
> String atomInfo =
> getJmolViewer().getAtomInfo(bitIndex++);
> System.err.println("Viewer.extractArray atomInfo: "
> + atomInfo);
> }
> return arrayList.toArray(new String[0]);
> }
>
> class MySelectionListener implements JmolSelectionListener
> {
> BitSet selectionBitSet = null;
> public BitSet getSelectionBitSet()
> {
> return this.selectionBitSet;
> }
>
> public synchronized void selectionChanged(BitSet
> selectionBitSet)
> {
> this.selectionBitSet = (BitSet)
> selectionBitSet.clone();
> }
>
> }
>
> Viewer.getMoleculeElements script: select none; select water; ---
> SHOULD PRODUCE ON WATER
> Viewer.extractArray atomInfo: [LYS]1:A.H1 #10
> Viewer.extractArray atomInfo: [ARG]21:A.HH21 #341
> Viewer.extractArray atomInfo: [THR]40:A.OG1 #613
> Viewer.extractArray atomInfo: [THR]40:A.HG1 #618
> Viewer.extractArray atomInfo: [SER]50:A.OG #753
> Viewer.extractArray atomInfo: [SER]50:A.HG #758
> Viewer.extractArray atomInfo: [ASN]59:A.HD22 #900
> Viewer.extractArray atomInfo: [SER]60:A.HG #911
> Viewer.extractArray atomInfo: [THR]69:A.OG1 #1056
> Viewer.extractArray atomInfo: [THR]69:A.HG1 #1061
> Viewer.extractArray atomInfo: [SER]100:A.OG #1502
> Viewer.extractArray atomInfo: [SER]100:A.HG #1507
> Viewer.extractArray atomInfo: [HOH]130:A.O #1962
> Viewer.extractArray atomInfo: [HOH]130:A.H1 #1963
> Viewer.extractArray atomInfo: [HOH]130:A.H2 #1964
> Viewer.extractArray atomInfo: [HOH]131:A.O #1965
> Viewer.extractArray atomInfo: [HOH]131:A.H1 #1966
> Viewer.extractArray atomInfo: [HOH]131:A.H2 #1967
> Viewer.extractArray atomInfo: [HOH]132:A.O #1968
> Viewer.extractArray atomInfo: [HOH]132:A.H1 #1969
> Viewer.extractArray atomInfo: [HOH]132:A.H2 #1970
> Viewer.extractArray atomInfo: [HOH]133:A.O #1971
> Viewer.extractArray atomInfo: [HOH]133:A.H1 #1972
> Viewer.extractArray atomInfo: [HOH]133:A.H2 #1973
> Viewer.extractArray atomInfo: [HOH]134:A.O #1974
> Viewer.extractArray atomInfo: [HOH]134:A.H1 #1975
> Viewer.extractArray atomInfo: [HOH]134:A.H2 #1976
>
> Viewer.getMoleculeElements script: select none; select hetero xor
> water; --- SHOULDN'T PRODUCE ANYTHING
> Viewer.extractArray atomInfo: [LYS]1:A.H1 #10
> Viewer.extractArray atomInfo: [ARG]21:A.HH21 #341
> Viewer.extractArray atomInfo: [THR]40:A.OG1 #613
> Viewer.extractArray atomInfo: [THR]40:A.HG1 #618
> Viewer.extractArray atomInfo: [SER]50:A.OG #753
> Viewer.extractArray atomInfo: [SER]50:A.HG #758
> Viewer.extractArray atomInfo: [ASN]59:A.HD22 #900
> Viewer.extractArray atomInfo: [SER]60:A.HG #911
> Viewer.extractArray atomInfo: [THR]69:A.OG1 #1056
> Viewer.extractArray atomInfo: [THR]69:A.HG1 #1061
> Viewer.extractArray atomInfo: [SER]100:A.OG #1502
> Viewer.extractArray atomInfo: [SER]100:A.HG #1507
>
>
>
> ------------------------------------------------------------------------------
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
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is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
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