-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Robbie,
maybe it is good not to use coordinates for calculations if you cannot measure the coordinates? Cheers, Tim On 06/13/2014 12:35 PM, Robbie Joosten 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 >> > 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/ iD8DBQFTmuJyUxlJ7aRr7hoRAjdqAJ95tqbDlWhqW01lAuVvLwsMIAkv1wCaA0Bk O0z7t7Bl7O7amDF9CxM0CI0= =QSdy -----END PGP SIGNATURE-----
