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 echo myEcho4 0 100%; echo First Line;
>>>>> set echo myEcho5 0 100%; echo "|Second Line"; //no overlap due to the
>>>>> initial newline (|)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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>>>>
>>>>
>>>> --
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>>>> SumoBrain: Intellectual Property Solutions & Data
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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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>
>
> --
> 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
>
>
--
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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