Hi Tim, The problem with missing atoms in ligands is that you cannot use the coordinates for any follow-up calculation that requires ligand topology (e.g. restraint generation). That forces you to rely on the annotation of the compound, for instance at the PDB. That can be quite messy and leaves extra room for errors and misunderstandings.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Tim Gruene > Sent: Friday, June 13, 2014 12:04 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Invisible atoms in ligands > > -----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/ > > iD8DBQFTmsx7UxlJ7aRr7hoRAhxOAJ9YXwdr4kZULidLAdzTgEjdZwfXNQCeKYT > A > 9vSeeDh7eq2v4CwBII64wn8= > =uviV > -----END PGP SIGNATURE-----
