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
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