Dear Luciano,
Here is my suggestion. I may not have all this right and I am certainly
willing to be corrected and learn from others!
When javascript wants to get information from Jmol about the currently
loaded model(s), I think the best method is, in javascript:
jmolEvaluate("jmol expression");
This function is defined in Jmol2.js, packaged with the Jmol download.
The value of the jmol expression will be returned to javascript.
This Jmol command reports the sequence in one-letter code, separately
for each chain:
print {protein}.find("sequence")
So in javascript, I think this will work (but I haven't tested it):
jmolEvaluate("{chain=a}.find(\"sequence\")");
This, of course, reports the sequence of residues that have coordinates.
It will not include the sequences of portions of the expressed
crystallized protein chain with missing residues due to crystallographic
disorder. Determining that sequence, as far as I know, requires parsing
the SEQRES records in the PDB file header (or the appropriate place in
the mmCIF file-- remember PDB format is going to be phased out by the
Protein Data Bank in favor of what they call PDBx which is just another
name for mmCIF format). (PDBe has the best sequence report showing
missing residues greyed out, e.g.
http://www.ebi.ac.uk/pdbe-srv/view/entry/1D66/primary.html --
FirstGlance in Jmol reports the number of missing residues in each chain
along with the number of missing + and - charges in each chain, and the
sequence ranges that are missing. In the Molecule Information Tab, click
on Missing Residues.)
For example, in 2ace, residues 485-489 are missing. PDBe reports:
N P N E P H S Q E S
K W P
Jmol's find("sequence") reports this as follows:
...NPNE //* 484 *//.
//* chain A protein 490 *// ~p~SKWP...
I have used jmolEvaluate() extensively in FirstGlance in Jmol, for
example to count various kinds of atoms. You will see some of those
reports in the Molecule Information Tab (first tab) in FirstGlance.
==========
MESSAGECALLBACK
I have used message callback extensively in FirstGlance in Jmol, mostly
way back with early versions of Jmol (but the code is still in there and
isn't broken so hasn't been "fixed"). I think it is best used when
javascript is waiting for some event in Jmol to happen, rather than when
javascript simply wants to ask a direct question. The message callback
function can watch the callback stream and take appropriate action in
javascript when the desired event happens and is reported in that stream.
I'll be happy to try to answer specific questions if they fall within
the 5% of Jmol that I understand :)
Kudos to Bob Hanson for creating the other 95% which remains for me to
discover and be astonished and delighted with!
And for keeping Jmol almost 100% backward compatible!
-Eric
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- Martz.MolviZ.Org <http://Martz.MolviZ.Org>
* Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
* FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
<http://firstglance.jmol.Org>
* Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.Org>
* Education: Biochem in 3D at MolviZ.Org <http://MolviZ.Org>
* Find Functional Patches in Proteins: ConSurf <http://consurf.tau.ac.il>
* Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.MolviZ.Org>
* Interactive Molecules in Architectural Spaces:
MolecularPlayground.Org <http://molecularplayground.Org>
* Workshops: Workshops.MolviZ.Org <http://workshops.MolviZ.Org>
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