-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Robbie,
Frank probably meant the status of the model when the author is ready for deposition, i.e., already after additional refinement. The B-factor assumes a harmonic oscillation of its atom on a linear trajectory (maybe the superposition of one trajectory in each of the three dimensions) - that's almost always a very poor assumption for an atom for which you don't see the density, and by using the B-value to mop up, you only adjust a parameter and may reduce the R-value, i.e. improve your model w.r.t. crystallographic data. As you remove the atoms you don't see, you improve your model with respect to its usability after deposition. Cheers, Tim On 06/13/2014 01:59 PM, Robbie Joosten wrote: > 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 >> > 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/ iD8DBQFTmuzWUxlJ7aRr7hoRAsazAJ0bkmlFBRPNxDDOnvuzRp9y5FMYBwCg3yj0 XosHt98UyfOcUrW4OWizoow= =YDU4 -----END PGP SIGNATURE-----
