The dots not changing color is certainly a bug that will be fixed in
10.9.47 (later today).
As for the action of restrict, this is intentional. (That is, a feature,
not a bug.) Let's discuss what we really mean by dots. Here's the deal:
Note that dots do not simply surround an atom. They take into account
neighboring atoms. Thus, unlike spacefill, dots are not just displayed,
they are the result of a rather complex calculation -- essentially the
solvent-accessible-surface calculation. (They are not quite the
solvent-accessible surface, because they do not take into account all the
other atoms around the selected set. isosurface sasurface takes this
into account, but dots does not. In fact, select *;dots +1.2 IS the
solvent-accessible surface.)
(Oh, I do so hate restrict!)
I'll look into whether restrict could properly restrict to part of the dot
surface, but the thinking on the part of Miguel and me up until now is
that since dots depend upon neighbors, and restrict changes neighborhoods,
dots should be completely removed if a restrict command is given.
The basic problem is that the following two will be different (which might
be OK):
select *;
dots on;
restrict (atomno 10);
# this would be a partial surface, like the action of sasurface?
restrict (atomno 10);
dots on;
# this would be a continous surface around those atoms.
Bob
First, any restrict command (including restrict not none and restrict
all, which do not affect any renderings that I know of except dots) hides
ALL dots. It seems to me that using restrict to hide a subset of atoms
should not hide ALL dots -- it should hide dots only for the set hidden --
just as it does for spacefill, etc.
Second, dots off hides ALL dots, even when preceded with select none.
Working around these bugs in FirstGlance in Jmol has required adding a lot
of messy javascript. It would be great to have them fixed!
Thanks, -Eric
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz
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