biomolecule oriented Jmol users: OK, I'm convinced by my colleagues here at St. Olaf and Carleton that this is HUGE. Just playing with it a bit, I'm totally excited. You can now load a subset of the atoms in a PDB file into Jmol (a limited SELECT sort of filter to the LOAD command that works at the file-reading level for PDB files) and then also select one of the BIOMOLECULE specifications in the "REMARK 350" biological unit section of the header and apply the symmetry described in that header.
Thank you to Eric, Rolf, and Dan for suggesting this. I believe that the next version of Jmol you see, 11.5.32, will have this working correctly. I've done a navigation mode fly-through of the entire 60-unit simian virus (1sva.pdb) looking at helices and sheets as I flew, and I'm sold. On my 1.2Gb-memory laptop Jmol rotates 124,000 atoms with cartoons like nothing in real time. So I think we are onto something. Now, interface. What do you want? I presume a menu entry under the main "symmetry" entry should be the place to start. What options do you need? -- option to replace or append? -- option to apply symmetry? -- list of biomolecules available (with # of atoms involved if symmetry is applied?) anything else on that menu? I suspect as people play with this more, they will want me to expand on that load filter select option. What else? Bob -- 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
