At the moment Garib is manually curating the dictionaries, so I forward
this to him.
B
-------- Original Message --------
Subject: Error in Chiral Centers in bacteriopheophytin a (BPH)
Date: Wed, 28 Mar 2012 10:35:50 -0700
From: Dale Tronrud <[log in to unmask]>
Reply-To: Dale Tronrud <[log in to unmask]>
To: <[log in to unmask]>
It was just pointed out to me that there is an error in the cif
in Coot for BPH. The two chiral centers in the phytol tail, C8 and
C13, are inverted. I'm including a cif with the correct definitions.
As an example you can check out the BPH residues in 2J8C. These
chiral centers are correct in the model, but Coot will invert them.
Oddly enough the matching chiral centers in this model's BCL molecules
are wrong but Coot fixes them. In Coot BCL is correct, BPH is not.
I'll have to check all the chlorophyll-like molecule definitions
in Coot but it will take me a bit of time. Bad chiral centers are
endemic for chlorophyll molecules in the PDB so it is very hard to
be sure you are looking at something that makes sense. What I'm
sure of is that the chiral centers of the BCL's in 3EOJ are correct.
It's based on 1.3 A X-ray data and you don't need chiral restraints.
Since all phytol tails are the same you can compare any chlorophyll-like
molecule to the tails in this model to see if you are correct.
Dale Tronrud
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