It seems that this thread got lost.
I did send Bob a test file; will send it again now.
11.6.RC13_dev still draws type 4 bonds (aromatic) as alternating double-
single. I don't like that.
Type 8 are dotted or partial, which
I suspect the behavior with 4 may be intentional, is it so? And how can I
make them look aromatic?
(maybe with the aromatic command? or was it calculate? I never catched
it)
On 17 Jul 2008 at 0:25, Bob Hanson wrote:
I'll need some specific file examples, please.
Angel Herráez wrote:
According to a previous report of mine (which went into doc. in the Wiki)
http://www.mail-archive.com/[EMAIL PROTECTED]/msg09232.html
in MOL format files, bond type 8 (described as any) used to be interpreted
by Jmol as
partial bond. Now I see it is not so; bond is not drawn.
I'd like to know if this is intended, or I was wrong, or it is a bug in
recent versions.
11.5.46 and 11.4.5 do not draw any bonds for type 8
11.3.11 draws them as partially double, or no bond, depending on the atom or
its
neighbors?.
I understand that since MDL doc does not assign partial meaning to type 8,
if may be more
sensible for Jmol not to interpret as so. However, no bond at all where a
bond is specified is
not a faithful solution either.
While I am at it, I also see that type 4 (aromatic) is rendered as partially
double by 11.3.11
but as alternating single and double bonds by 11.4.5. I guess that's a
conscious
consequence of the recent aromatic and calculate aromatic commands,
right?
I'd rather prefer that the aromatic-specified bonds are drawn as partially
double, but I won't
push for it. Just want to mention is case it is an inadvertent change.
Well, there's even more. Here's a summary across versions:
bond type 4
11.3.11: aromatic (partially double)
11.4.5: alernating single and double bonds
11.5.46dev (8 july 08): aromatic (partially double)
bond type 8
11.3.11: partially double !!
11.4.5: no bond
11.5.46dev (8 july 08): no bond in some cases, double in others!!
I also note that in 11.5.46, some single bonds are drawn as double
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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