On Sun, Jun 30, 2013 at 10:17 PM, James <james@ryley.com> wrote:
Are .hin comments (designated by a line starting with a semicolon) available as a variable in jmol, or should I just parse them directly (e.g., from getProperty fileContents)?

You should parse them. If you are having any problem with HIN files let me know. Haven't done anything with that reader in a long long time.

And, the Jmol wiki says:
"at# is the number identifying the atom in the molecule (must start with 1 and be continuous through a molecule). Therefore a combination of atom number and molecule number uniquely identifies an atom in a file. "
Does that mean that, unlike I believe can occur with a pdb, .hin atom numbers are never arbitrarily changed? Or, does it just mean "At any given time, there is a unique combination, but that combination is not guaranteed to be the same from time to time (e.g., if you add or delete atoms)"?

There is something called "atomIndex" that goes from 0 to the end of all files read. Each atom has a distinct number in this.
There is something else called "atomNo" that is pulled in from the file. This could have duplicates in a file or across multiple files.

Deleting atoms does not change either of these numbers.


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Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN

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