Bob,
I'm pretty sure the atomno's were different. I found this because a script that
used to work failed - e.g. selection of a bond between two atoms in one of two
models in the window. If you look at the molfile of the models, it's a single
model molfile. I'm pretty sure that previous versions (not sure when this
happened) had atomno's that corresponded to the atom position in this single
model molfile.
To be clear, this is a result of load append with loadappend set to false. If I
load butane and then load append acetone, they share the atomno's 1, 2, etc.
This all may be a moot point. The atom indexes are unique, and I should
probably be using them anyway. Users who use atomno's in scripting may want to
take note of the email exchange, however.
Related point: I'm having a horrible time with my conformation rotation script
on the new Safari (rotation freezes the model and breaks scripting). That's why
I updated Jmol. I'm still trying to find this Safari problem. I'll get back to
you if I can't solve it.
FYI, the script is as follows. The variables rot1 and rot2 are atomno's set by
a bond click. This works fine on Chrome. It breaks scripting on the new Safari.
set Picking OFF;set Picking ON;set BondPicking TRUE;set atomPicking TRUE;set
allowRotateSelected TRUE;unbind "SHIFT-DRAG"; bind "SHIFT-DRAG" "select
WITHIN(BRANCH,{atomno=rot1}, {atomno=rot2}); if (_X < 250){select
WITHIN(BRANCH,{atomno=rot2}, {atomno=rot1});} rotateSelected {atomno=rot1}
{atomno=rot2} @{_DELTAY}";hover off;
Otis
--
Otis Rothenberger
[email protected]
http://chemagic.com
On Nov 1, 2013, at 7:55 AM, Robert Hanson <[email protected]> wrote:
> Sounds right to me, Otis. They should have the same atom numbers because they
> are the same model.
>
> Are you saying this behavior is different with previous versions? I don't
> think so. Let me know if that's the case.
>
> If you want to assign different atom numbers, you can do that:
>
> var lastOld = {*}/2
> for (var i = {*}; i > lastOld;i--) { {*}[i].atomno += lastOld }
>
> Bob
>
>
>
> On Thu, Oct 31, 2013 at 11:26 PM, Otis Rothenberger <[email protected]>
> wrote:
> Bob,
>
> I recently installed 13.3.8_dev_2013.10.29. In the course of trying to find a
> nasty conformation rotation bug in my code, I found a problem with loadappend.
>
> Go to http://chemagic.com/JSmolVMK.htm. Duplicate (link) the default model.
> These two models have identical atomno's - e.g. select atomno=1;color pink
>
> The "duplicate" link on this page appends with set loadappend = false.
>
> The extracted molfile looks OK, but the scripting atomno's are both 1 to 15.
>
> Otis
>
> --
> Otis Rothenberger
> [email protected]
> http://chemagic.com
>
>
>
>
>
>
>
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>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
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