Mauricio Carrillo Tripp wrote: > Bob Hanson wrote: >> The different sets of atoms >> created by individual BIOMT transformations are selectable using the >> "symop" selection option: >> >> select symop=3 >> select symop<6 >> >> etc. (There is a bug there -- symop=1 specifically is not selectable in >> 11.5.32) > > > OK, so for example, if I want to display 1/2 capsid, I will have to load > the PDB file 30 times, each time using a different select in the loading > filter. > By using the append option in the load command, all 30 biomolecules > will 'live' on different frames, which can be independently selected by > frame, OR the symop operator. correct? >
We must be careful not to mix up terms here. As far as I understood the "biomolecule" is always a whole biologically active unit. In the case of Mauricio's virus capsid there is only a single biomolecule and it consists of the asymmetric unit plus 59 copies generated by symmetry operations. In the case of PDB entry '4otb' there are 6 different biomolecules which all look very similar. Each biomolecule consists of different sets of 2 chains (out of 12) from the asymmetric unit plus 2 copies of these chains generated by symmetry operations. So in the end you will have 6 slightly different hexamers if you generate all biomolecules. As far as Bob has described the filter options yet, I don't think that it is currently possible to apply only a subset of the symmetry operations of a specific biomolecule. So with the virus capsid you would always get 60 copies of whatever you selected by the filter (e.g. only 1 chain out of 3) into a single model/frame. And if you wanted to display only only one half of the capsid you could use for example the following command: display symop<=30 How this half would really look like would of course depend on the order of the symmetry operations (e.g.: a ball might look afterwards like a ball with holes and not like one half of a ball). Regards, Rolf ------------------------------------------------------------------------- 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
