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" <[email protected]> wrote:
On Thu, Jan 14, 2010 at 1:07 PM, Grossman, Robert B <[email protected]>
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
------------------------------------------------------------------------------
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
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
