Thanks Bob that works nicely and it even does C=O.
However there is a problem with the popup window feature. It shows the
version with every bond aromatic rather than the desired version with
only double bonds. This can be fixed by "calculate aromatic" on the
new window but it spoils the effect of the popup window.
I found that connect aromatic auto seems better in that regard. The
popup window is now fine
Any ideas why these two behave differently with the popup window and,
is there a downside to using connect aromatic auto?
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
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On 3 Apr 2008, at 07:43, [EMAIL PROTECTED] wrote:
Date: Wed, 02 Apr 2008 23:00:10 -0500
From: Bob Hanson <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Automatic generation of multiple bond types
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Nick Greeves wrote:
Is there a command which will generate multiple bond types (even just
double would be a start) from a structure that lacks such info e.g.
.xyz ?
It's
select {*} // maybe
connect aromatic modify
calculate aromatic
The idea is that aromatic systems are conjugated systems, and Jmol
knows
how to follow the conjugated single/double sets in a clever way to
always produce the best set of double bonds (if there is one).
You can actually select all the atoms, but I don't recommend it,
because
that might throw off minimization. What I was doing for caffeine was:
select connected(2) or connected(3) or oxygen and connected(1)
At least that was good enough for caffeine. A general solution would
be
somewhat more specific -- connected(3) and (not nitrogen or nitrogen
and
connected({oxygen})) -- something like that. You want to include the
carbonyls even though they are not technically aromatic.
Bob
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