I need some help testing Jmol. If you use PyMol, perhaps you can compare
Jmol's COMPARE command to PyMol's pair_fit command.
http://www.pymolwiki.org/index.php/Pair_Fit
I think with PyMol it's a bit more tedius in that you need to specify EVERY
pair of atoms, but in any case we don't need too many, I think. Just a few
pairs on whatever system you want to look at to see if Jmol is giving the
same result.
where in PyMol you would give
pair_fit {selection1} {selection2} {selection1} {selection2} {selection1}
{selection2} ...
in Jmol you would use, after loading two models if you only what to pair up
the alpha carbons -- which would be the simpler thing for this test:
compare {2.1} {1.1} {3-5.CA} rotate translate
if you are just pairing residues 3 4 5, or
compare {2.1} {1.1} {3-5.CA} {10-12.CA} rotate translate
if you are mapping differently numbered sets.
Thanks,
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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