Re: [ccp4bb]: Difficulties with refmac5 dictionary usage: Problem #2

[Liz Potterton <lizp@ysbl.york.ac.uk>]

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Hi Ethan,

Just one quick comment about using Sketcher..when you import a PDB  you
need to set the bond types.  For aromatic rings you need to define a
Kekule structure with alternate double and single bonds.  This is a pain
but easier than adding hydrogen atoms which is (sort of) equivalent
information.

The problem that you dscribe is that Libcheck is interpreting the ring
as aromatic when it is not.  This might just be a knock on effect of not
giving the correct bond type for substituents. Could you send us your
PDB file for us to give it a try?

Liz