Dan Bolser wrote: >The thing is that the PDB is the central archive of all protein >structure data. They provide (or attempt to provide) the BioUnit data >in the PDB header. It seems reasonable to want to view the data 'at >its source' with whatever visualization tool you like best. Its true >that you can obtain the data elsewhere, but you may not know what went >into its production. For example, the BioUnit data in the MSD database >has had a lot of undocumented manual clean-up. > > > Right, so Jmol 11.5.32 is now reading that header.
>Also, I would also generally like to try applying different symmetry >operations to the data. This would be the case when the PDB BioUnit >was not correct (or appeared not to be correct). For example, Pisa >gives a variety of different results for a given PDB. It would be >really nice if I could easily generate these in Jmol without having to >grab each file from Pisa separately ... although perhaps the latter is >the easiest option. > > > I think you can do all that now, as of this morning. The PDB header specifies a set of 4x4 rotation/translation matrices. Do you have a way of generating those matrices yourself? Maybe not. One thing you can do with ANY file loaded into Jmol is to define a unit cell and spacegroup (or set of "Jones-Faithful" symmetry operations -- x, -y, z+0.5 -- that sort of thing) and apply the symmetry to the model as it loads. So if I were interested in trying different symmetries, I would probably do it that way. Basically the LOAD command options UNITCELL and SPACEGROUP allow you to over-ride the file-based data. That seems to be what you are interested in, Dan. Or you can use it to apply symmetry to files that have no symmetry data included. (I suspect to do this effectively we might have to add an ORIGIN parameter that would allow an initial translation of the data.) I don't think anyone but me has realized this option to date, so not much has been developed in this area. Now that we have the option to load a specific subset of the data (a specific set of chains, really), you can load just the chain you are interested in and have at it with changing the symmetry and such. Let me know if that interests you. Bob >HTH, > >Dan. > > > >> Bob >> >> >> >> Dan Bolser wrote: >> >> >Bob: Some friends and I tried to answer that question (what is a >> >BioUnit?) as part of a 'PDB FAQ' that we have been working on. We >> >thought that this question was important and complex enough to get a >> >page all to itself. You can see what we currently have here: >> > >> >http://pdbwiki.org/index.php/Biological_unit >> > >> > >> > >> That's pretty much what I understood. >> >> >> >ftp://ftp.wwpdb.org/pub/pdb/data >> > >> > >> >Under this branch you can find exactly the data that you want. Namely, >> >the results of applying the symmetry operations in remark 350 to the >> >ASU. >> > >> > >> > >> > >> >> >> >>>Dan. >>> >>> >> > >> > >> > >> > >> > >> >>------------------------------------------------------------------------- >> >> 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 >> >> >> >> >> >> >> >> >> > >> > >> > >> > >> >> >> -- >> >>Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >> ------------------------------------------------------------------------- >> >> >>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 >> >> >> > > > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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
