Hi Tim, The problem I see with including atoms with no density is that the one place you can guarantee those atoms are not (at 100% occupancy), is at the coordinates assigned to them. I would argue that the scientific inaccuracy of such a model should outweigh the desire to use the coordinates for downstream calculations.
A better solution may be for the PDB to require us to submit the PDB and CIF file we generate for the full ligand in addition to the protein PDB file which may only contain a truncated portion of the ligand as part of the model. I prefer omitting the atoms in the same way I do for the protein model and for the same reasons. I accept this makes it potentially more troublesome for downstream users as things stand, although would argue that there is greater potential for harm if the unsuspecting user believes the atomic positions are correct, where a ligand (or protein) atom has been modeled into a region with no density. Best, Isaac Westwood > > >> On 13 June 2014 11:35, Robbie Joosten <robbie_joos...@hotmail.com> wrote: >> >>> 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----- >>> >> >> >
