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------------------------------------xx----------------------------------------- Jmol users: The numbers are flying fast because of minor bugs we are finding and the desire to get them fixed and onto the Sourceforge site as quickly as we can. This announcement covers 10.9.74-10.9.76. display/hide/displayed/hidden ----------------------------- Jmol 10.9.76 introduces something I've wished Jmol had for a LONG time -- a friendly, reversible "restrict" option. So, here it is. I believe this makes "restrict" obsolete. (But don't worry, we won't removed "restrict"!) These commands behave much like "select". Four new keywords are introduced: display hide displayed hidden so we have: display */1 or */3 # display just models 1 and 3 display all # return to full display display hidden # show the complement of what is displayed hide displayed # same thing hide hidden # nothing new, but it displays how many atoms are hidden hide hidden or _Fe # add iron to the hidden set hide hidden and not _O # remove oxygen from the hidden set display molecule=1 # do exactly that display within(molecule,symop=3) # This one is a bit tricky -- it first selects for a certain symmetry operation (such as -x, y+1/2, z), and then it adds to that any atom in the connected set. So you get a full molecule, not just a piece of one. configuration for cif --------------------- I've changed the name of "conformation" to "configuration" because I think it is a more general term (maybe) -- I'm leaving "conformation" in there still -- and with display, it's terrific: configuration 1 # selects altloc undefined or altloc first listed display selected color altloc # red for constant, green or blue for alternate locations Note that for PDB or mmCIF models, "configuration" also recalculates the secondary structure based on the revised set of group atom positions. Then it returns the selected set. popup menu ---------- Major revisions should make this actually useful -- it is now highly dynamic, changing with each model viewed using "frame" or "model", and updating to reflect such things as whether it's a PDB file, what it's HETATM groups are, lists of configurations, molecular orbitals, options for displaying symmetry, correct listing of atoms and bonds. More to come on this (lists of symmetry operations, for example). Your input appreciated. One possibility is that this popup menu can (also) be a part of the console as a fixed menu bar. Good idea? Not? history and #-- --------------- There are still issues to be resolved here. My goal is to get Jmol to the point where you can always see a record of what commands were given, no matter how they are given -- from the pop-up menu, from the application toolbar, or from atom picking. We have a ways to go on that, but I've now identified all the issues and am slowly making my way through them. As of 10.9.76 anything you do from the popup menu is added to the history. Typing the word "history" at the command prompt now delivers the history of all commands given. For those who have scripts that you want run but you do NOT want added to the command history, just add "#--" to the end of each line of the script you want ignored. That line of commands will be run, just not added to the script history. --Bob Hanson ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
