Thanks, Peter. Yes, that's a killer. Definitely not ready to read 16,000,000
atoms! But I have added a new option that lets you load some smaller number
of biomolecule transformations. Looks like we'll have to let Rolf open that
one for us.... ;)
On Mon, Apr 5, 2010 at 11:22 AM, Peter Rose <pwr...@ucsd.edu> wrote:
> Hi Bob,
>
>
>
> I believe 1M4X is the largest biomolecule in the PDB
> http://www.pdb.org/pdb/explore/explore.do?structureId=1M4X.
>
>
>
> -Peter
>
>
>
> *From:* Robert Hanson [mailto:hans...@stolaf.edu]
> *Sent:* Sunday, April 04, 2010 8:09 PM
>
> *To:* jmol-users@lists.sourceforge.net
> *Cc:* Rose, Peter; David Goodsell; Miguel
> *Subject:* Re: Jmol -- two major advances
>
>
>
> 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
>
--
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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