On 9 Oct 2006 at 7:40, Bob Hanson wrote: > ignore(solvent) is fine; the "1.2" isn't allowed right now. The "1.2" > refers to the solvent probe radius which, again, in my conceptualization > of this as a general command, isn't always applicable.
A fixed radius for "molecular" is OK to me; I just understood form your previous message that you could not filter errors if parameters were allowed differently. I think there is a point in having a simple command like "isosurface molecular" just so > I made it 1.4 simply because I'm seeing that a lot more > than 1.2 in current discussions. Do you have a feeling for that -- does > half the world use 1.2 and the other 1.4, or is 1.2 "old school"? No particular preference. Yes, I also think people use 1.4 most commonly. It's only the old Rasmol inheritance of 1.2 still there. In fact, Chime adheres to 1.2 for dots and set solvent, but uses 1.4 for surfaces. I think I've read that 1.2 is meant size of oxygen, while 1.4 accounts for the 2 hydrogens in water, more realistic, or that is has something to do with accounting for the molecule having hydrogens or not. Anyway, I wouldn't bother; anyone that knows what (s)he is doing will impose the radius wanted, while for a general purpose surface is not much difference. 1.4 gives a smoother molecular surface, which is good. In fact, maybe having both 1.2 and 1.4 in the pop-up menu is going too far. I think the menu must be cleaned up. How about leaving sasurface 1.2, solvent 1.2 and molecular 1.4 only? > wanted a simpler alternative to "solvent [radius]" but if you think > that's splitting hairs and just making it confusing, I could change the > default to 1.2 and allow for "molecular [radius]". No need, as discussed above. (More about the colors on the menu on separate thread) ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
