OK, that's in now:
http://chemapps.stolaf.edu/jmol/Jmol-13.zip
___JmolVersion="13.1.19_dev_2013.06.29"
new feature: SET ECHO POINT {atom or point}
-- allows 2D and 3D echos to have a pointer to an atom or a specified
position such as {0 2.0 3.0}
-- needs a bit of adjustment, as it only works when x is not within range
of echo itself (same with labels)
On Sat, Jun 29, 2013 at 10:43 PM, James <[email protected]> wrote:
> For my purposes that would be by far the simplest I think.
>
> Sincerely,
> James
>
> On Saturday, June 29, 2013, Robert Hanson wrote:
>
>> Would you prefer having a 2D echo that is tied to an atom by a pointer?
>>
>>
>> On Sat, Jun 29, 2013 at 10:40 PM, Robert Hanson <[email protected]>wrote:
>>
>> It's much different from what existed in 13.0. In that version all you
>> can do is move a label a small distance in pixels.
>>
>> 1) you can put any offset of any size in for a label.
>> 2) you can offset in molecular coordinates (ax, ay, az) or in "screen"
>> (sx, sy, sz) coordinates.
>>
>> I think the only thing it doesn't do is let you make labels, like echos,
>> adjust for window boundaries.
>>
>>
>>
>>
>> On Sat, Jun 29, 2013 at 9:44 PM, James <[email protected]> wrote:
>>
>> How is that different than what exists? Perhaps in that it is applied
>> post-rotation? That would make it a bit simpler, assuming the offset can be
>> large enough to place the label anywhere.
>>
>> I think I could, with a little ugliness, make the current labels work if
>> the offset could be > 127. Or, I could use absolute scaling, try to
>> figure out where the screen boundary approximately is in angstroms, and use
>> that to draw an arrow from an echo to an atom. Anything that would reduce
>> the ugliness would be good lol.
>>
>> Thanks,
>> James
>>
>>
>> On Saturday, June 29, 2013, Robert Hanson wrote:
>>
>> That's right. There isn't a way to draw from a fixed point on the
>> screen to an atom. You might try a recent addition in relation to PyMOL.
>> This is a much more general offset method that is used in PyMOL and I
>> needed to implement in Jmol, so we have it as well now.
>>
>> Do give this a try and let me know if it solves your problem:
>>
>> new feature: PyMOL-like label offset options:
>>
>> set labelOffset [sx, sy, sz]
>> set labelOffset [mode, sx, sy, sz, ax, ay, az]
>>
>> where
>>
>> sx,sy,sz are screen coord offsets
>> -- in Angstroms
>> -- applied after view rotation
>> -- sy > 0 LOWERS label
>> ax,ay,az are xyz position (in Angstroms; applied before view rotation)
>> mode == 1 indicates xyz position is an offset to the atom position
>> mode != 1 indicates xyz position is absolute
>> defaults: mode == 1; ax = ay = az = 0
>>
>> Note that those sx sy sz are not in pixels, they are in angstroms. Also,
>> I note that there is a bug that disallows label pointers with this sort of
>> offset. Hmm....
>>
>>
>>
>>
>>
>> On Sat, Jun 29, 2013 at 1:50 PM, James <[email protected]> wrote:
>>
>> Thanks Angel. I see that echo has almost everything. But, the reason I
>> was trying to use labels is because they can have a line to an atom. After
>> reviewing "draw ARROW" in the hopes that it could substitute for that line,
>> I don't see that it is possible to draw from a 2D point (e.g., top left) to
>> a 3D point (an atom). I tried assigning echo an ID and drawing from that to
>> an atom, but (as I suspected - just hoping I could trick it) since echo
>> isn't a draw object it doesn't work. I can't find a way to bridge that
>> 2D/3D coordinate issue, which label does automatically.
>>
>> Thanks,
>> James
>>
>>
>> On Saturday, June 29, 2013, Angel Herráez wrote:
>>
>> Hello, James
>>
>> By definition, labels are attached to atoms. That is why the distance
>> cannot
>> be long.
>> >From your description, I don't think that labels are what you need. You
>> have
>> "echo" for positioning text either in 2D screen space or in 3D molecular
>> coordinates, at arbitrary positions and with chosen alignment, even
>> multi-line.
>>
>> e.g.
>>
>> set echo myEcho1 0 50%; echo Hello;
>> // windowLeft+windowMiddle, left flushed
>> set echo myEcho2 0 100%; echo Good Bye;
>> // windowLeft+windowTop, left flushed
>> set echo myEcho3 15% 85%; set echo center; echo Another;
>> // close to windowLeft+windowTop, center-justified
>> // note that text will never go out of screen, it will flush to the edge
>> if needed
>>
>> set e
>>
>>
>
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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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