Thanks, Eric.
The exact operation of restrict in 10.00.48 consists of:
a) invert the selection
b) set the bondmode to OR temporarily
c) set all selected bonds to wireframe 0
d) return the bondmode setting to its original value
e) turn off all labels of selected atoms
f) turn off all selectable shapes (balls, cartoons, etc.)
g) invert the selection back to its original setting
Eric Martz wrote:
It seems to me that "restrict not x" should have the same effect as
"select x; [display] off". That is, both should hide the display
(wireframe, backbone, trace, cartoon) of the atomset x. This is true
for some, but not for other displays; the latter cases seem to me to
be bugs.
well, it's different. Restrict is "stronger" in the sense that any bonds
to the removed atoms are also hidden.
-----------------------------
Problem 1, restrict not vs. wireframe & bondmode: Suppose you display
some DNA with wireframe. The command "restrict not phosphorus" makes
all the phosphorus-oxygen bonds disappear. This happens regardless of
"set bondmode and/or". This seems to me to be a bug: the
phosphorus-oxygen bonds should disappear after "restrict not
phosphorus" only after "set bondmode or".
the above sequence explains this behavior.
---------------------------------
Problem 2, restrict not vs. backbone and bondmode: I want to hide a
single residue in a protein or nucleic acid backbone with "restrict
not [residue]". This works for trace and cartoon (which do not obey
bondmode), but not for backbone. For backbone, you have to "restrict
not" two consecutive residues before a gap appears in the backbone.
Ah, Good catch. This is a bug. It is fixed by switching steps (d) and
(f) above.
I've uploaded these changes; the jar files in my prototype site can be
tested; I find
select *;backbone 1.0
restrict not SER
works correctly -- two single-residue gaps.
these corrections are in:
http://www.stolaf.edu/people/hansonr/jmol/test/json/
for now.
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