Hens wrote: > And about the bonds: > >>Q: Do you want to be able to control the order of >>*existing bonds*, or do you want to be able to create >>*new* bonds? >> >> > Let's say existing bonds, although I can imagine it could be useful to > define a bond where Jmol doesn't suspect one. > But I don't have a real example of that at the moment.
OK. Since you are generally working with .pdb files then changing existing bonds makes sense. Some of the 'inorganic' folks who work with *strange* elements have asked about creating bonds. >>Q: After removing some bonds and adding others, do you >>want to be able to return to the original? >> > A kind of reset you mean? > Didn't think of that. My idea would that if I create one by a script, > I'll remove it by a script. After changing bonds orders would you expect to be able to restore them back to the original state with one command. That would probably be painful for me to implement. >>Q: What file types? pdb? (this shouldn't matter too much). >> > Well, mainly the types in which no bonds are defined, like xyz and pdb. > The way to define double bonds in the CONECT recordsof the latter is not > straightforward if I remember well from the Chime discussions, don't > know how Jmol reads this records. Jmol supports this CONECT convention just fine. It is very straightforward ... if you connect the atoms twice then it is a double-bond ... 3 times -> triple bond. I am puzzled that the Chime discussion list found it complicated. > But then, once you have a structure displayed, the scripts should work > independent of the original file type, shouldn't they? Correct. So, what do people think about this ... We introduce a new scripting command called 'bondOrder'. bondOrder [ 1 | 2 | 3 | aromatic | hbond ] It applies to all pre-existing bonds within the current set of selected atoms ... just like 'wireframe' It respects the 'set bondmode [ and | or ] ' setting ... just like 'wireframe' Q: Is there a word other than 'bondOrder' that we should use? Miguel ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] ----- ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
