On May 10, 2006, at 10:35 AM, Miguel wrote:
Some time ago I did some prototyping where I put all of the altLoc atoms
in the same model. One of the first things that I saw was that the
'autobond' code that builds connectivity just fell apart. Places where
there altLoc atoms just turned into a knot of spaghetti.
This is one of the things that made me think that it was necessary to
build separate models. But, the number of distinct models quickly gets too
large.
I could well be missing something(s), but I think a simple straightforward
solution to the handling of altLoc's should be possible.
The PRIMARY objectives as I see it are:
1. Enable users to select altLocs with complete flexibility. A user should
be able to select and display concurrently e.g. altLoc A at residue 50,
altLoc B at residue 100, altLoc C at residue 150, and altLoc A at residue
200; or any arbitrary permutation.
2. It should also be easy to select all altLoc A's as a group; or all
altLoc B's as a group, etc.
3. Inappropriate covalent bonds must be avoided (no spaghetti, basket
weave, or birds nests).
[Chime can do none of 1, 2, or 3. It shows all altLocs as spaghetti.]
These objectives seem to me to contribute to simplification of
IMPLEMENTATION as follows:
4. It is fine to handle, internally within Jmol, all altLoc A's as one
"model" (but using different selection/display syntax than for NMR
MODEL/ENDMDL models), all altLoc B's as a different "model", etc.
Permutations can be handled by selection/display commands. There is no need
to have all possible permutations listed internally somehow. (I believe
that a long time ago I may have objected to this concept. If so, I have
changed my mind.)
5. Handling A's as a distinct model from B's, distinct from C's, and
prohibiting bonds between altLoc-models takes care of spaghetti.
RECOMMENDATIONS:
6. It will often be sufficient to display all altLoc A's, then hide A's and
display B's, then return to A's, so as to toggle back and forth. Item #2
above enables this mode of "toggling" display. Of course, if the user wants
to toggle arbitrary permutations, they can do so using the residue-specific
altLoc selection as in #1 above.
7. I am in favor having all altLocs displayed concurrently in the initial
default view of Jmol. This avoids having people be unaware of the altLocs.
On Jmol's menu could be a new AltLoc's section. The default would be "All
altLocs", with other options being A, or B, or C (listing only those that
actually exist in the loaded model). (Display of permutations would need to
be handled with custom scripting.) Another menu item could be "animate
altLocs" which would show each "model" (A, B, C) in turn for half a second
or so. These menu options would handle 95% of people's needs, I suspect.
-Eric
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