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
Paul, also note that the Jmol state is incldued in those PNG or JPG files,
so you can just drag and drop them into Jmol or use
script file.png
There is an issue there with directory paths. The latest rendition of Jmol
strips all local paths off but leaves the web-based paths. when reading
these
How do you decide on how pyramidal (or not) to make a N Bob? What about
hydroxyl H atoms when there is the potential for intramolecular H-bonding?
Rich
On Fri, 15 Jan 2010 11:01:22 -0600, Robert Hanson hans...@stolaf.edu
wrote:
OK, that's in. See Jmol 11.9.19 ---
Robert Hanson escribió:
calculate hydrogen # adds the hydrogen atoms to C,N,O,and S atoms,
respecting bonding but not considering formal charge (for now).
This sounds exciting, Bob!
minimize addHydrogens # minimizes and then adds H atoms at the end
I have one wonder here. In my
We'll have to experiment. You could add some but not all -- just select the
atoms you want to add the hydrogens to. As implemented, Jmol will not add
MORE hydrogens to any atom already bearing hydrogens.
-- oh, the latest has formal charge added. I don't know about radicals.
Mostly we need to
(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
Le 14 janv. 2010 à 20:07, Grossman, Robert B a écrit :
(2) Save image of the current view. The best format would be PNG. Yes, I
can do a screen capture of a view with another program, but that's extra work.
That feature exists. You've got two options :
- using the signed applet, you
Bob, the problem with saving images or whatever is that Java applets are not
allowed to
access the user's disk. That's why the signed applet exists, and can do it, as
Paul has said.
- using the signed applet, you can send the script
save IMAGE PNG filepath/imagename.png
And apart from
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
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.
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