Dear all, thanks for your comments and sorry for the late reply. I am using the digest mode and hence I only get a summary.
Rolf: Unfortunately the "set autobond on" does not work for me.
Angel:
On Dienstag 31 Januar 2017 jmol-users-requ...@lists.sourceforge.net wrote:
> XYZ files do not include bond information, while MOL and MOL2 do.
> So I guess your C--P distances are above what Jmol considers "bonded"
> Maybe you can change the default value of
>
> set bondTolerance (decimal)
> "When autobonding, the value of bondTolerance is added to the two bond
> radii of atoms being tested for a bond. A larger bondTolerance allows
> atoms that are further apart than the sum of their listed radii to still
> be bonded. This parameter should be adjusted prior to file loading for
> proper maintaining of the Jmol state."
>
> Other possible ways to fix that:
>
> {_P}.bondingRadius =
>
> set bondingVersion
>
> data "element_vdw" 6 1.7; 7 1.8 END "element_vdw"
What worked well in my case is this:
set bondTolerance =1.005
That draws the C-P bond quite nicely and does not mess up the benzene rings I
have.
So thanks for that.
Robert: Although that does work, it is messing up the benzene ring so I get
nice bonds drawn where there clearly is no bond inside the ring.
In any case, many thanks for this it was really helpful!
All the best from a mild London
Jörg
--
*************************************************************
Dr. Jörg Saßmannshausen, MRSC
University College London
Department of Chemistry
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