Hi Tim, The decision of which atoms you can and cannot see in your map is rather subjective. Also the way you generate your map can make a big (enough) difference. A new map after additional refinement, an NCS averaged map, or a feature-enhanced map might show you the position of (some of) the missing atoms. I prefer the 'high B-factor' model unless you have a very good reason to believe the compound is in any way chemically modified.
Cheers, Robbie > -----Original Message----- > From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] > Sent: Friday, June 13, 2014 13:37 > To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Invisible atoms in ligands > > -----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/ > > iD8DBQFTmuJyUxlJ7aRr7hoRAjdqAJ95tqbDlWhqW01lAuVvLwsMIAkv1wCaA0 > Bk > O0z7t7Bl7O7amDF9CxM0CI0= > =QSdy > -----END PGP SIGNATURE-----
