> The other issue is distinguishing hbonds as calculated > and as file-determined. We should be able to selectively > display/undisplay these.
I agree. The same applies to regular bonds as well. > Something associated > with the hbond mask should do the trick here. Good point. Maybe we can set a bit in the order field to say whether or not that bond was 'original' Good topic for discussion later. > Miguel wrote: >> >> When we set the size on an hbond, the hbond calculation >> code is being run because it has never run before. > > This is fine. Just don't run the calculation if setting > the size = 0. If setting the size positive, it's pretty > clear that one is asking for the calculation. I guess my explanation wasn't clear. I think that is part of the problem. One creates their own hbonds using 'connect hbond ...'. They then change the size of their hbonds. I don't think that the 'hbond calc' code should run. This problem existed in trunk200603 and in the current trunk. Q: Bob, do you agree that this is a problem, or am I missing something? > It seems to me no big deal. (But see below) > >> >> Once the hbond calculation code has been run, it will never >> run again ... even if we do a 'connect delete hbond ...' >> because the hbond code does not >> currently know that hbonds can be deleted. >> > > Obviously we need > > hbonds calculate > > which might have two flavors -- Rasmol and Jmol, for example. > > >> My thoughts: >> >> * we need to separate hbond size control from hbond autocalculation > > I don't see any great need for this. The two are already > separated; we need that default action. Something else > must be wrong here. Try the following ... with either trunk200603 or with the current trunk load 1CRN.pdb connect hbond (1.O)(1.N) hbond 0.25 I don't think that it is giving us the desired result. Take a look and let me know what you think Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
