2008/4/28 Bob Hanson <[EMAIL PROTECTED]>: > Dan, Eric, Rolf, > > First, if Jmol implemented this it would do so at the file load stage -- > as some sort of option to the LOAD command. That's because all symmetry > is applied during the process of file loading, not after. I'm guessing > there are some pretty serious GOTCHA!s in doing this. Can't be simple. > > Second, am I understanding that there are servers that do this already? > If so, why should we do this in Jmol? Why not just point people to > services that do this already, and then suggest using Jmol to read the > already-constructed files?
Hey Bob, Nice pictures! 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. 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. 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 > -- hello ------------------------------------------------------------------------- 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
