Re: [ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis
Hello Chandrika, you can either set the occupancy of the molecule to 0.5 and refine it as a whole molecule or leave the occupancy at 1, refine only one half of the molecule and let the symmetry operator do the rest. Chemically the first way makes more sense to me: even though the PEG molecule sits on the symmetry axis, it may nevertheless not follow the two-fold symmetry. The lattice is built by the macromolecule, and much can happen in the space inbetween - even though in that case you would probably have to deal with disorder. When you deposit the structure you should do it depending on which of the two above methods you chose. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Wed, 29 Apr 2009, Chandrika Deshpande wrote: Hello everyone, My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes two problems which I need to solve : First, How can I refine this structure ? I am using Phenix. Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ? Second, how do I submit this structure to PDB ? Do I include a full PEG molecule at half occupancy even though one half is related to the other via crystallographic symmetry ? Thanks, Chandrika
Re: [ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis
Hi everyone, Following Chandrika's question, what should I do if one peptide chain crosses a two-fold crystallographic symmetry axis? The peptide is not symmetric and the sidechain of one Se-Met (two after CS operation) is determined and conformed by MAD. Your sincerely De-Feng Li lidef...@moon.ibp.ac.cn 2009-04-29 Defeng Li, Dr., Email: lidef...@moon.ibp.ac.cn National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China === 2009-04-29 17:02:00 You writed in your letter：=== Hello everyone, My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes two problems which I need to solve : First, How can I refine this structure ? I am using Phenix. Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ? Second, how do I submit this structure to PDB ? Do I include a full PEG molecule at half occupancy even though one half is related to the other via crystallographic symmetry ? Thanks, Chandrika
