Re: [Jmol-users] Support of Alchemy format

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

Definitely no alchemy file format reader in Jmol. If someone can find
me a specification, I'll create one. I'm a little concerned that the
file format does not specify element -- assuming, for example, that
"CAR" will be interpreted as carbon. I'd need to know what other
aspects like that there might be that would complicate the reader.

Bob


On Mon, Dec 8, 2008 at 7:42 AM, Angel Herráez <ang...@ua...> wrote:
> Does Jmol really support the Alchemy format?
>
> The Jmol main webpage does not mention it, the Jmol Wiki does (both are likely my
> fault). However, there are no example files in "Jmol-datafiles" folder at SVN.
>
> I tried the non-chemical file just reported by Xiang-Jun Lu and a molecule from Paul
> Bourke (linked from the Wiki {1}). The Jmol Java Console says
>         The Resolver thinks FoldingXyz
>
> and reports
>  13 atoms, 10 bonds where the file says 12 atoms, 12 bonds
> and
>  22 atoms, 17 bonds where the file says 21 atoms, 21 bonds
>
>
> {1}
> http://wiki.jmol.org:81/index.php/File_formats#Alchemy_.28Tripos.29
> http://local.wasp.uwa.edu.au/~pbourke/dataformats/alc/alc3/
>
>
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-- 
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