Jmol users,
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.17.zip
adds the feature of calculating the smallest box that can contain a
selected set of atoms. It is only an approximation, using 1495
pre-calculated quaternion-based orientations, but I think it is pretty
good. On my machine,
Hi Bob
Interesting. I'm still guessing what this would be useful for but, since you
mention the box, it could be nice to have a way to draw that box also, with or
without the rotation.
?
--
Get 100% visibility into
For example, your database shows structures. What's the best default
orientation to show such that the longest side of the box is along X and
the shortest depth is toward the user?
rotate BEST
Bob
On Sun, Aug 18, 2013 at 4:57 AM, Angel Herráez wrote:
> Hi Bob
>
> Interesting. I'm still guess
On 08/19/2013 02:10 AM, Robert Hanson wrote:
> For example, your database shows structures. What's the best default
> orientation to show such that the longest side of the box is along X and
> the shortest depth is toward the user?
>
> rotate BEST
>
I thought that this might be an intended usage. B
On 08/19/2013 01:19 PM, Rolf Huehne wrote:
> On 08/19/2013 02:10 AM, Robert Hanson wrote:
>> For example, your database shows structures. What's the best default
>> orientation to show such that the longest side of the box is along X and
>> the shortest depth is toward the user?
>>
>> rotate BEST
>
On 08/19/2013 01:19 PM, Rolf Huehne wrote:
> On 08/19/2013 02:10 AM, Robert Hanson wrote:
>> For example, your database shows structures. What's the best default
>> orientation to show such that the longest side of the box is along X and
>> the shortest depth is toward the user?
>>
>> rotate BEST
>
What's your algorithm for that, Rolf?
--
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, Mo
Am 19.08.2013 23:55, schrieb Robert Hanson:
> What's your algorithm for that, Rolf?
>
The idea is to bring the largest boundbox plane to the front.
So first the x,y and z boundbox vector length is determined.
Then for each possible case the required rotations are done.
Since I developed the algori
Sure.
rotate BEST
does more than simple 90-degree rotations. Could be different definitions
of what is "best" of course. What it has now is "smallest volume with
thinnest side directed toward the user and longest side along X."
Were you sure to select the same set of atoms as you did in your al
On 08/20/2013 01:18 AM, Robert Hanson wrote:
> Sure.
>
> rotate BEST
>
> does more than simple 90-degree rotations. Could be different definitions
> of what is "best" of course. What it has now is "smallest volume with
> thinnest side directed toward the user and longest side along X."
>
> Were yo
Hmm. Shouldn't work that way. ROTATE BEST initializes with a "restore
orientation" (or, at least it effectively does that, because it multiplies
in the inverse of the current rotation quaternion).
What was the exact sequence of commands you used there? As far as I know,
the only way it can give a
On 08/20/2013 04:20 PM, Robert Hanson wrote:
> Hmm. Shouldn't work that way. ROTATE BEST initializes with a "restore
> orientation" (or, at least it effectively does that, because it multiplies
> in the inverse of the current rotation quaternion).
>
> What was the exact sequence of commands you use
Rolf,
console problem -- yes, I saw that on a Mac last weekend. I'll look into
it. Something about the way the mouse events are being handled in Safari, I
think. Can you try Firefox or Very frustrating!
rotate: sorry, I can't reproduce that, hard as I try.
Rotate BEST
executes this:
q
On 08/20/2013 06:43 PM, Robert Hanson wrote:
> Rolf,
>
> console problem -- yes, I saw that on a Mac last weekend. I'll look into
> it. Something about the way the mouse events are being handled in Safari, I
> think. Can you try Firefox or Very frustrating!
>
I am not using Safari. I am using Firef
I found it. A bug in the new JSmoljQueryExt.js that allows JSmol now to be
used with user-provided jQuery if desired.
See http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.20b.zip
I think that fixes the mouse problem -- or at least it should get rid of
that stream of messages coming from jQ
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