Re: [Jmol-developers] MolFile errors

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

David,

Where's your third coordinate? Are these 2D mol files? If so, they are not
identifying themselves as such in the second line. See, for example,
http://c4.cabrillo.edu/404/ctfile.pdf, particularly Chapters 2 and 4. These
are rigidly formatted files. For example, the atom lines must be of the
following format, as described in Chapter 2:

xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee

I think your file doesn't have that format, from the looks of it.

Bob






On Sun, Feb 3, 2013 at 4:21 PM, N David Brown <hu...@gm...> wrote:

> After quickly writing a MolFile generator for some fictional structures,
> the generated MolFile strings load acceptably in Jmol but produce several
> error lines containing '0 0' is not a recognized symbol.
>
> Any idea why? Here's an example file:
>
> unknown
> NDB/matchbOx/03022013221425
>
>  4 4 0 0 0 0 0 0 0 0 1 V2000
>    0.0000 0.0000 0 C 0 0 0 0 0 0 0 0 0 0 0 0
>    0.0000 1.0000 0 C 0 0 0 0 0 0 0 0 0 0 0 0
>    1.0000 0.0000 0 C 0 0 0 0 0 0 0 0 0 0 0 0
>    1.0000 1.0000 0 C 0 0 0 0 0 0 0 0 0 0 0 0
>  1 4 1 0 0 0 0
>  1 2 1 0 0 0 0
>  2 3 1 0 0 0 0
>  3 4 1 0 0 0 0
> M END
> $$$$
>
> Even the cited benzene example here<http://en.wikipedia.org/wiki/Chemical_table_file>generates a ''
> is not a recognized symbol.
>
> David
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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