minor point -- 4rhv (rhinovirus) biomolecule 1 (full capsid, all 392,520
atoms) loads just fine. I was just loading it in the programming environment
rather than the applet and thought there was some sort of limitation, but it
appears that was not real.
HEADER RIBOSOME 18-JUL-07
2QNH
TITLE INTERACTIONS AND DYNAMICS OF THE SHINE-DALGARNO HELIX IN
THE
TITLE 2 70S RIBOSOME. THIS FILE, 2QNH, CONTAINS THE 30S
RIBOSOME
TITLE 3 SUBUNIT, TWO TRNA, AND MRNA MOLECULES. 50S RIBOSOME
SUBUNIT
TITLE 4 IS IN THE FILE
1VSP.
SPLIT 2QNH
1VSP
test: load five copies of the combined files (t.pdb)
$ load t.pdb;select *
147,125 atoms selected
$ load append t.pdb;select *
294,250 atoms selected
$ load append t.pdb;select *
441,375 atoms selected
$ load append t.pdb;select *
588,500 atoms selected
$ load append t.pdb;select *
735,625 atoms selected
frame *;cartoons on
$ isosurface sasurface
isosurface1 created with cutoff=0.0; number of isosurfaces = 1
$ display none
735625 atoms hidden
At this point the rotation is a bit sluggish. But I'm not seeing the memory
issue anymore. So I'm starting to think that Jmol has no practical limit to
the number of atoms loaded. Is that possible? My memory indicator is reading
257 Mb.
Question: What's the largest model in the PDB database?
Bob
On Sat, Apr 3, 2010 at 10:59 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Jmol users and RCSB/PDB aficionados,
>
> Something for everybody here
>
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
>
> contains a version of Jmol -- 12.0.RC3_dev -- that some of you may be
> interested in, and I'm very much interested in your testing.
>
>
> 1) Mega-size PDB files
> 2) true hydrogen bonds
>
>
> I'm aiming for a Jmol 12.0 release for June 1. In the mean time -- test,
> test, test!
>
>
> 1) Mega-size PDB files.
>
> Jmol 12.0.RC3_dev will load considerably larger files than Jmol 11.8. I
> don't know the exact limit; I've loaded 90 copies of hemoglobin -- 409,950
> atoms total, and there doesn't seem to be a problem. Obviously there IS a
> limit... But that task required 148Mb of memory when I went to "cartoons
> only", and there wasn't any real problem. (OK, I admit that displaying all
> the models, the rotation was a bit jerky.) The composite ribosome 2qnh+1vsp
> with full atoms was no problem. I do note that I still cannot get the whole
> rhinovirus 4rhv loaded as a full capsid -- 392520 atoms -- so maybe there is
> still something I am missing. Or maybe that hemoglobin example was just at
> the limit. In any case, this is quite an improvement, I think.
>
> I thank Wayne Decatur for getting me thinking about this. I've had a
> suspicion for some time that there had to be something wrong. It turns out
> the problem was that during loading Jmol was creating two full copies of the
> data. That is no longer necessary -- obviously not necessary!
>
> Also, and please tell me if this is a major problem -- I've set it to load
> like Rasmol (wireframe only) when there are more than 40,000 atoms. That may
> be too few, but my guess is that mostly people don't need ball&stick for an
> initial load of so many atoms. I can already see a problem -- if you load a
> large alpha-carbon only file, then you see nothing! How about backbone only
> for that?
>
> 2) true hydrogen bonds
>
> It's been on the list for a long time. Now it's here. Thanks to Eric Martz
> for getting me onto this one.
>
> calculate HBONDS
>
> does pretty much what you would expect it to do for "normal"
> (hydrogen-containing) models. See the documentation.
> http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=12.0#calculate
> "Standard" PDB files will still calculate hydrogen bonds using the DSSP
> method provided they have no H atoms or you select no H atoms when you do
> the calculation. But now there are more options. DSSP "energies" are
> calculated for all hydrogen bonds that are calculated. I don't put much
> confidence in the meaningfulness of that number, but it is there, anyway.
>
>
> Bob
>
>
> --
> 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
>
--
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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