Actually, if you go back through the archive of CCP4-BB from the first time this came up, I think you'll find that there are real crystals with apparent gaps in the packing. This can arise because of statistical disorder, where there are two or more ways that a statistically-disordered layer in the crystal can mediate the interaction between ordered layers. So not finding a connected packing is something to look closely at and worry about, but it doesn't necessarily indicate that somebody did a bad job of making up a structure.
Randy On 6 Feb 2015, at 11:09, Robbie Joosten <[email protected]> wrote: > Not in real crystal structures ;) > > Cheers, > Robbie > > Sent with my Windows Phone > Van: Kerff Fred > Verzonden: 6-2-2015 12:02 > Aan: [email protected] > Onderwerp: [ccp4bb] Absence of contact between layers in a crystal > > Hello, > > Looking at structure 2HR0 ("The structure of complement C3b provides insights > into complement activation and regulation. »,Abdul Ajees, A., Gunasekaran, > K., Volanakis, J.E., Narayana, S.V., Kotwal, G.J., Krishna Murthy, H.M.; > (2006) Nature 444: 221-225), I noticed the absence of contacts between layers > in the crystal. Is it something that has already been observed in other > crystals? > > Best regards, > > Fred > ----- > Frédéric Kerff > Chercheur qualifié F.R.S.-FNRS > Cristallographie des protéines > Centre d'Ingénierie des Protéines > Université de Liège > 17, Allée du 6 Août - Bat B5a > 4000 Liège (Belgium) > Tel.: +32 (0)4 3663620 > Fax: +32 (0)4 3663772 > > > > > Le 6 févr. 2015 à 10:12, Tim Gruene <[email protected]> a écrit : > > > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > Dear Smith, > > > > The sca file most likely does not contain flags. pointless can read > > the sca file, standardise it to ccp4 standards and freerflag marks > > random reflections. You should use the maximum of 500 unique > > reflections or 5% of the unique reflections, whichever is larger. > > > > Best, > > Tim > > > > On 02/06/2015 09:49 AM, Smith Lee wrote: > >> Dear All, I have a sca file. Will you please tell me by which > >> software or how I can know whether the sca file contains R-free > >> tags? If not, by which software or how I can add the R-free tags? > >> And how much of the reflections I add the R-free tags? I am looking > >> forward to getting your reply. Smith > >> > > > > - -- > > - -- > > 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) > > > > iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi > > j0JFZac4kAh8twpov71MG84= > > =XN57 > > -----END PGP SIGNATURE----- ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
