OK, that's in. See Jmol 11.9.19 ---
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
calculate hydrogen # adds the hydrogen atoms to C,N,O,and S atoms,
respecting bonding but not considering formal charge (for now).
minimize addHydrogens # minimizes and then adds H atoms at the end
delete {hydrogen} # does that
Bob
On Thu, Jan 14, 2010 at 9:14 PM, Grossman, Robert B <robert.gross...@uky.edu
> wrote:
> My suggestion would be that if a multiple bond is not specified, you should
> assume a single bond, and if a charge or radical is not specified, you
> should assume enough H atoms to give the atom its octet. If the user is not
> specifying multiple bonds, then he simply shouldn't use the function.
>
> Consider the MOL file below. Some H atoms are specified, some not. I had
> Jmol do a minimization, and it correctly deplanarized the isopropyl group.
> If it can do that, then it can easily position the H atoms.
>
>
> Marvin 03180516593D
>
> 22 22 0 0 0 0 999 V2000
> -0.4201 0.2577 -1.4146 C 0 0 0 0 0 0 0 0 0 6 0 0
> 1.0119 0.6024 -0.9257 C 0 0 2 0 0 0 0 0 0 5 0 0
> 1.4430 -0.3157 0.2489 C 0 0 2 0 0 0 0 0 0 4 0 0
> 0.4201 -0.2577 1.4146 C 0 0 0 0 0 0 0 0 0 3 0 0
> -1.0119 -0.6024 0.9257 C 0 0 0 0 0 0 0 0 0 2 0 0
> -1.4430 0.3157 -0.2489 C 0 0 0 0 0 0 0 0 0 1 0 0
> -0.7193 0.9460 -2.2082 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.4212 -0.7482 -1.8450 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.7207 0.5093 -1.7516 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5221 -1.3462 -0.1098 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7193 -0.9460 2.2082 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.4212 0.7482 1.8450 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.7207 -0.5093 1.7516 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0386 -1.6454 0.5961 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5221 1.3462 0.1098 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.4331 0.0241 -0.6065 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.8389 0.0954 0.7531 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.0495 2.0704 -0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.3832 2.8404 -0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.2742 2.8574 -0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.1725 -0.6746 0.7531 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.4409 -0.0177 1.3286 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 1 6 1 0 0 0 0
> 2 3 1 0 0 0 0
> 3 4 1 0 0 0 0
> 4 5 1 0 0 0 0
> 5 6 1 0 0 0 0
> 1 7 1 0 0 0 0
> 1 8 1 0 0 0 0
> 2 9 1 0 0 0 0
> 2 18 1 0 0 0 0
> 3 17 1 0 0 0 0
> 3 10 1 0 0 0 0
> 4 11 1 0 0 0 0
> 4 12 1 0 0 0 0
> 5 13 1 0 0 0 0
> 5 14 1 0 0 0 0
> 6 15 1 0 0 0 0
> 6 16 1 0 0 0 0
> 17 21 1 0 0 0 0
> 18 19 1 0 0 0 0
> 18 20 1 0 0 0 0
> 21 22 1 0 0 0 0
> M END
>
>
>
> On 1/14/10 9:42 PM, "Robert Hanson" <hans...@stolaf.edu> wrote:
>
>
>
> On Thu, Jan 14, 2010 at 1:07 PM, Grossman, Robert B <
> robert.gross...@uky.edu> wrote:
> (1) Display H atoms. If I load a structure that does not show H atoms, it
> would be nice to have Jmol calculate their positions and display them. I
> know it must know that they are there, because when I loaded a structure
> with a planar C the the center of an isopropyl group, then minimized the
> structure, it converted the C to tetrahedral. (I guess it's possible you
> have this feature, but I'm not able to find it.)
>
> Jmol doesn't know they are there. The UFF calculation is simply optimizing
> the single-bond C-framework. If the problem can be better defined, we might
> be able to do something about it. Certainly would be a good trick. Do you
> have the bonding already -- double, triple? One problem, for example, is:
>
> C -C-O
>
> is that CH3CH2OH? CH2CH2OH? CH2C=O? CH3CHO? If the bonding is there, then
> we are ok; if it is not, then
>
> But if you have double bonds, it's easy. Send me a file.
>
> Bob
>
>
>
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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
------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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