I'm not seeing the problem with 12.1.23_dev. If a carbon is sp2-hybridized,
as indicated here by the planar geometry, Jmol will correctly not add H
atoms to that position. The correct load if you want to convert 2D to 3D is:
load sample1.mol FILTER "2D"
This will attempt to add hydrogen atoms and minimize the structure upon
loading.
Bob
2010/11/14 Angel Herráez <angel.herr...@uah.es>
> While testing 2D to 3D conversion with random drawn structures, I've
> noticed that Jmol
> sometimes fails to calculate a hydrogen for a carbon that has 3
> substituents.
> Today an example has shown this dramatically.
>
> I am using "minimize addHydrogens" or just "calculate hydrogens" with same
> result. Tested
> now on 12.1.13 and 12.1.21, probably also other versions.
>
> The data is loaded into Jmol unsigned applet as text in 2D MOL format using
> loadinline, but
> I've just verified that saving to a file and loading it into Jmol app does
> the same.
>
> Example (also attached):
> ------------------
>
> Ketcher 11141015152D 1 1.00000 0.00000 0
>
> 14 15 0 0 0 999 V2000
> -1.1250 0.2250 0.0000 C 0 0 0 0 0 0 0 0 0 0
> -0.2340 -0.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0
> -0.2340 -1.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0
> -1.1250 -1.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0
> -1.9910 -1.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0
> -1.9910 -0.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0
> 0.7171 0.0340 0.0000 C 0 0 0 0 0 0 0 0 0 0
> 1.3049 -0.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0
> 0.7171 -1.5840 0.0000 C 0 0 0 0 0 0 0 0 0 0
> -1.1311 1.2250 0.0000 C 0 0 0 0 0 0 0 0 0 0
> -0.2682 1.7303 0.0000 C 0 0 0 0 0 0 0 0 0 0
> -2.0002 1.7197 0.0000 C 0 0 0 0 0 0 0 0 0 0
> 1.0261 0.9851 0.0000 N 0 0 0 0 0 0 0 0 0 0
> 2.3049 -0.7750 0.0000 O 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0
> 2 3 1 0 0 0
> 3 4 1 0 0 0
> 4 5 1 0 0 0
> 5 6 1 0 0 0
> 6 1 1 0 0 0
> 2 7 1 0 0 0
> 7 8 1 0 0 0
> 8 9 1 0 0 0
> 9 3 1 0 0 0
> 1 10 1 0 0 0
> 10 11 1 0 0 0
> 10 12 1 0 0 0
> 7 13 1 1 0 0
> 8 14 1 1 0 0
> M END
> ------------------
>
>
> The following section of this message contains a file attachment
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>
> ---- File information -----------
> File: sample1.mol
> Date: 14 Nov 2010, 15:16
> Size: 1446 bytes.
> Type: Unknown
>
>
> ------------------------------------------------------------------------------
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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
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Simplifying enterprise desktop deployment and management using
Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
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