Hi All,

I had an interesting case recently where a Cl atom of a chlorophenyl moiety went missing in a structure (primary X-ray damage was the suspected culprit). Small molecule Mass Spec suggested the atom was there to start with but it was quite obviously missing in the maps (1.9Ang) and the des-chloro refined much better. I was asked to replace the missing atom as it was seen as misleading because all the assay and biophysical data was generated with the chlorophenyl compound; this after all, is what the X-ray model was supporting. I did wonder where the Cl atom ended up and in what state.

David Hargreaves

Associate Principal Scientist

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AstraZeneca

Discovery Sciences, Structure & Biophysics

Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF

Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693

David.Hargreaves @astrazeneca.com

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From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Frank von Delft
Sent: 13 June 2014 10:45
To: [log in to unmask]
Subject: [ccp4bb] Invisible atoms in ligands

Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them?

For bits of protein, I know all the arguments; personally I prefer omitting atoms because:

for amino acid sidechains, their presence is implied in the residue name.
for whole residues, their presence is implied in the sequence numbering

However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something?

(Certainly disorder in a ligand is important information that needs to be captured!)

Cheers
phx