-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Frank,
if you can calculate their position, i.e. it is part of a rigid group, I would leave it. If it is flexible, I would remove it because the reader of my deposited structure may not be a crystallographer and misinterpret the result. If it is obvious that some atoms are missing, it is even better because it is more likely to make the reader think about the reasons why part of the ligand is not displayed in the model. Cheers, Tim On 06/13/2014 11:45 AM, Frank von Delft wrote: > 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 > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTmsx7UxlJ7aRr7hoRAhxOAJ9YXwdr4kZULidLAdzTgEjdZwfXNQCeKYTA 9vSeeDh7eq2v4CwBII64wn8= =uviV -----END PGP SIGNATURE-----
