[Jmol-developers] anyone using load RANGE ?

[Bob H. <ha...@st...>]

I'm considering modifying the definition for LOAD RANGE. The current 
definition reads:

,'### load symmetry range ###'
,'# Jmol 11.3.9 introduces the capability of visualizing the close 
contacts around a crystalline protein (or any other cyrstal structure) 
that are to atoms that are in proteins in adjacent unit cells or 
adjacent to the protein itself. The option RANGE x, where x is a 
distance in angstroms, placed right after the braces containing the set 
of unit cells to load does this. The distance, if a positive number, is 
the maximum distance away from the closest atom in the {1 1 1} set. If 
the distance x is a negative number, then -x is the maximum distance 
from the {not symmetry} set. The difference is that in the first case 
the primary unit cell (555) is first filled as usual, using symmetry 
operators, and close contacts to this set are found. In the second case, 
only the file-based atoms (Jones-Faithful operator x,y,z) are initially 
included, then close contacts to that set are found. Depending upon the 
application, one or the other of these options may be desirable.'


What this allows is loading just the atoms near the unit cell or just 
the atoms near the file-based atoms. It is quite useful if you are 
interested in atoms in a crystal in close contact with atoms in the base 
atom set {not symmetry} or the atoms in the {1 1 1} set but don't want 
to load thousands of atoms you really are not interested in ever viewing.

OK, but that finding of the closest atoms is very time consuming. The 
change I've implemented speeds up the process immensely for PDB files in 
particular, because in the specific case of using a negative number to 
look for close atoms around the basic set of atoms in the file -- what 
you would always want for a PDB file -- then rather than checking every 
atom, we just look for atoms near a box containing those atoms:

,'### load symmetry range ###'
,'# Jmol 11.3.53 introduces the capability of visualizing the close 
contacts around a crystalline protein (or any other cyrstal structure) 
that are to atoms that are in proteins in adjacent unit cells or 
adjacent to the protein itself. The option RANGE x, where x is a 
distance in angstroms, placed right after the braces containing the set 
of unit cells to load does this. The distance, if a positive number, is 
the maximum distance away from the closest atom in the {1 1 1} set. If 
the distance x is a negative number, then -x is the maximum distance 
from a box just containing the {not symmetry} set. The difference is 
that in the first case the primary unit cell (555) is first filled as 
usual, using symmetry operators, and close contacts to this set are 
found. In the second case, only the file-based atoms (Jones-Faithful 
operator x,y,z) are initially included, and atoms sufficiently close to 
a box containing those atoms are loaded. Depending upon the application, 
one or the other of these options may be desirable.'

This is much faster, and then one can do the equivalent as described 
before using

  display within(2.0, !symmetry)

for example, to get exactly those atoms within 2.0 angstroms, say, of 
the actual atoms in the original atom set.

OK?

Bob

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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