I've checked in code for Jmol 11.9.34_dev
# new feature: COMPARE command (was ALIGN)
# compare {model1} {model2} [orientations]
# compare {model1} {model2} [orientations] {bsAtoms1} {bsAtoms2}
# compare {model1} {model2} [orientations] quaternionList1 quaternionList2
# additional options for above: ROTATE and/or TRANSLATE
# compare {model1} {model2} atoms {bsAtoms1} {bsAtoms2}
# additional options for above: TRANSLATE (not ROTATE yet)
OK, so what this does is compare two models and display RMSD values. The
ROTATE option rotates model1, and the TRANSLATE option translates model1.
But these are optional. Without them it just reports.
compare {model1} {model2} ORIENTATION
compares two model orientations based on quaternion frames. The ORIENTATION
keyword is optional. Valid frames are set using
set quaternionFrame "X"
where X determines the basis for the frames and is one of:
C alpha-carbon and nucleic base
P peptide carbonyl and nucleic backbone phosphorus
N peptide NH directed frames
compare {model1} {model2} ORIENTATIONS {bsAtoms1} {bsAtoms2}
compares two model orientations based on quaternion frames. The ORIENTATION
keyword is optional. Only frames for the specified sets of atoms will be
included. WIthout TRANSLATE or ROTATE, the two model specifications are
still necessary, because before operating, bsAtoms1 is ANDed with model1,
and bsAtoms2 is ANDed with model2. So, for example, one could say the
following to select only subsets of the models to base the analysis:
compare {1.1} {2.1} ORIENTATIONS {12-30} {32-50}
compare {model1} {model2} ORIENTATIONS quaternionList1 quaternionList2
compares two model orientations based on quaternion frames. The ORIENTATION
keyword is optional. Two arrays containing quaternions specify the data used
in the calculation. These can be created, for example, from specific sets of
residues:
var qset1 = quaternion({1-30/1.1})+quaternion({40-50/1.1})
var qset2 = quaternion({41-70/2.1})+quaternion({10-20/2.1})
compare {1.1} {2.1} ORIENTATIONS @qset1 @qset2
This allows precise specification of model residues for the comparison.
Without additional parameters ROTATE and/or TRANSLATE, the model
specifications are necessary for syntax only. They may be simply {} {}.
compare {model1} {model2} ATOMS
Does a simple RMSD calculation of the two models (after aligning centers of
mass). ROTATE is not implemented yet.
compare {model1} {model2} ATOMS {bsAtoms1} {bsAtoms2}
Does a simple RMSD calculation of the two atom sets bsAtoms1 and bsAtoms2
(after aligning centers of mass). WIthout TRANSLATE, the two model
specifications are still necessary, because before operating, bsAtoms1 is
ANDed with model1, and bsAtoms2 is ANDed with model2. ROTATE is not
implemented yet.
TODO: ATOMS ROTATE
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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