Quoting Bob Hanson <[EMAIL PROTECTED]>: > Jmol is not considering those remarks. Teach me about biounits. Are > these also in mmCIF files? >
The biological unit is supposed to resemble the biologically active form of a molecule (according to the believe of the authors). In very simple cases the asymmetric unit consists of a single protein monomer and in the biological unit a dimer or trimer is created by applying symmetry operations to the monomer. A more complicated case is entry "4OTB". In the "Chains,Units" Table of the corresponding JenaLib atlas page "http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=4otb&EXPAND=chains"; you can see that the asymmetric unit contains 12 protein chains. In the biological units these are reduced to 2 chains in a first step. In a second step these 2 chains are then copied twice to build a hexamer. And since there are six pairs of chains this results in 6 possible biological units. The information in the atlas pages on biological units is derived from biological unit PDB files that are provided by the PDB. Appareantly they have done what Dan and Eric would like Jmol to do: use the information provided by the authors to build the biologically active forms. This information is also provided in mmCIF files and in the case of "4OTB" it looks like this: loop_ _struct_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 2 ? ? 3 ? ? 4 ? ? 5 ? ? 6 ? ? # loop_ _struct_biol_gen.biol_id _struct_biol_gen.asym_id _struct_biol_gen.symmetry _struct_biol_gen.details _struct_biol_gen.pdbx_full_symmetry_operation _struct_biol_gen.pdbx_PDB_order 1 A 1_555 ? x,y,z 1 1 A 2_555 ? -y,x-y,z 1 1 A 3_555 ? -x+y,-x,z 1 1 D 1_555 ? x,y,z 2 1 D 2_555 ? -y,x-y,z 2 1 D 3_555 ? -x+y,-x,z 2 2 G 1_555 ? x,y,z 3 2 G 2_555 ? -y,x-y,z 3 2 G 3_555 ? -x+y,-x,z 3 2 J 1_555 ? x,y,z 4 2 J 2_555 ? -y,x-y,z 4 2 J 3_555 ? -x+y,-x,z 4 3 M 1_555 ? x,y,z 5 3 M 2_555 ? -y,x-y,z 5 3 M 3_555 ? -x+y,-x,z 5 3 P 1_555 ? x,y,z 6 3 P 2_555 ? -y,x-y,z 6 3 P 3_555 ? -x+y,-x,z 6 4 S 1_555 ? x,y,z 7 4 S 2_555 ? -y,x-y,z 7 4 S 3_555 ? -x+y,-x,z 7 4 V 1_555 ? x,y,z 8 4 V 2_555 ? -y,x-y,z 8 4 V 3_555 ? -x+y,-x,z 8 5 Y 1_555 ? x,y,z 9 5 Y 2_555 ? -y,x-y,z 9 5 Y 3_555 ? -x+y,-x,z 9 5 BA 1_555 ? x,y,z 10 5 BA 2_555 ? -y,x-y,z 10 5 BA 3_555 ? -x+y,-x,z 10 6 EA 1_555 ? x,y,z 11 6 EA 2_555 ? -y,x-y,z 11 6 EA 3_555 ? -x+y,-x,z 11 6 HA 1_555 ? x,y,z 12 6 HA 2_555 ? -y,x-y,z 12 6 HA 3_555 ? -x+y,-x,z 12 1 KA 1_555 ? x,y,z 13 1 KA 2_555 ? -y,x-y,z 13 1 KA 3_555 ? -x+y,-x,z 13 Regards, Rolf ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
