We are decidedly closer to 11.2. Nico has just released 11.1.42. All
testing appreciated.
version=11.1.42
# bug fix for lack of updating of certain variable predefined expressions
# bug fix for load append and structure commands
# bug fix for load files losing structure and cartoons
# bug fix for multiple frames displayed does not show Select...Elements menu
# bug fix for select @x not functioning where x = {atom expression} or x
= "atom expression"
# bug fix for {atom expression}.ident nonfunctional
# bug fix for smiles nonfunctional
Bug fixes:
---------
There are some issues that go way back with using CONNECT and SELECT
that still may not be fully resolved. They are subtle. We probably need
a better way of flushing definitions when changes occur. For example, if
you do the following:
load caffeine.xyz
define ch3 carbon and connected(3, hydrogen)
select ch3 # 3 atoms selected
connect (carbon) (hydrogen) delete
select ch3 # 3 atoms selected
You will see that Jmol selects the ORIGINAL set of atoms, not "nothing".
This is because when definitions are made, atoms are assigned once. This
makes for more efficient scripts. The same goes with "solvent" and
"helix". Once Jmol has carried out the calculation of the definition, it
saves the value and doesn't do it again. (You can change this behavior
by prepending "DYNAMIC_" to your definition.
load caffeine.xyz
define DYNAMIC_ch3 carbon and connected(3, hydrogen)
select ch3 # 3 atoms selected
connect (carbon) (hydrogen) delete
select ch3 # 0 atoms selected
So that was OK. But there was a bug that didn't properly update "helix",
for example, when one did "load append". The definition of "helix" was
still the original one from the original "load" command. I noticed this
while fixing the bug Frieda flagged, and fixed it as well.
Frieda had noticed that when two PDB files are loaded or a PDB file is
appended, biomolecular structure in the original file was lost. For
example, cartoons disappeared. This should be fixed. Now if you load
multiple files or append files, there should be no effect on the
structures already loaded. The "structure" command introduced in 11.1.41
is not necessary, but since it adds the capability to redefined what
residues are helix, sheet, and turn anytime and any number of times
after file loading, let's leave that in. This needs thorough testing.
Also in conjunction with this fix, I fixed the "calculate structure"
command to calculate structure only for the model in the current frame
or frames.
In addition, I noticed that {atom expression}.ident was not working, so
that is fixed, and while doing that, I realized that a simple addition
to the code would allow an interesting new capability in terms of
scripting. When you do the following:
x = {ala,thr}
Jmol returns the NUMBER of atoms as x:
x = 35
and the actual "set" of atoms as x_set:
x_set = "{ala,thr}"
(I know, should have been the actual set returned in x and then
something like x.count to get the number. Please don't ask me to change
this now.)
So then you could use the following syntax:
select x_set
I've been looking for a way around this, and I think I have it in
11.1.42. Now you can just ignore those "x_set" items and do the following:
x = {ala,thr}
select @x
And, in addition, you can do this with any string, since that's really
what "x_set" is, and this just uses x_set behind the scenes:
x = "{ala,thr}"
select @x
It's a subtle difference, but the advantage here is that then one can
create strings, manipulate them, and then later use them in SELECT
commands.
Finally, I accidentally incapacitated smiles parsing in 11.1.30. This is
restored.
Coding Changes
--------------
Jmol 11.1.42 involves a major reorganization of the Jmol code. In
particular, the biomolecular modeling code (backbone, cartoon,
meshribbon, ribbon, rockets, strands and trace, and the their associated
structural elements) has been completely overhauled, simplified, and
reorganized. This little exercise shows how far programming has come in
the last few years. There is no possible way this could have been done
efficiently without the programming tools we have now. (I use Eclipse.)
Even saved a few KB of space.
Bob
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