Another relatively frequent case concerns carbohydrates at the reducing end of a polysaccharide, where both alpha and beta anomeric forms can occur. Because the PDB gives two different CCD IDs to alpha and beta anomeric forms of the same monosaccharide – e.g. BGC and GLC for glucopyranose – you have the same problem described here. See Fig9 in https://journals.iucr.org/d/issues/2017/02/00/ba5257/ for an example (sorry for the plug!).
On Tue, 25 Jun 2019 at 16:00, Guenter Fritz < [email protected]> wrote: > Dear all, > thank you all for feedback help. > Best wishes! > Guenter > > Dear Guenter, yes look at crambin (pdbcode 1EJG). > > > This crashes Coot until you add* > > allow_duplicate_sequence_numbers() > > to $HOME/.coot.py in OSX or the appropriate place on Windows. For > Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/ > directory for configuration - these can be found (added to) the > directory in which Coot was installed (e.g. C:\WinCoot). > > To resolve your problem look at > > https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 > > example 5 > > Br, Georg. > > > Am 2019-06-24 um 4:22 PM schrieb Savvas Savvides: > > The structure of milk proteins obtained from in vivo-grown crystals from a > viviparous cockroach could also serve as an interesting case: > > http://dx.doi.org/10.1107/S2052252516008903 > > best wishes > Savvas > > > On 24 Jun 2019, at 16:03, Holton, James M < > [email protected]> wrote: > > A classic case of this is crambin. Residue 25 of 3nir. > > -James Holton > MAD Scientist > > On 6/24/2019 1:00 AM, Guenter Fritz wrote: > > Dear all, > > I am refining a multimer and mass spec data of the sample indicate > that there is a mixture of two variants which differ in one amino acid > residue. The density that we see is therefore most likely an average > of both variants. I have created a pdb file with "alternate residues" > each with 0.5 occupancy at this position to use it in refinement. > However, the programs detect this as an error in the pdb file. > > Has anyone faced such a problem previously? Any suggestions are very > much appreciated. > > Thanks a lot and best regards, Guenter > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- Dr Jon Agirre Royal Society University Research Fellow York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8252 Twitter: @glycojones ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
