Menu
▾
▴
#630 with set 3d echo, letters appear at wrong position
Hi
In newer versions of JSmol, the coordinates used to set 3d echo are different from the coordinates of atoms and polyhedra. For example, an atom with coordinates {0 0 0} and a letter with coordinates {0 0 0} are displayed at different positions. Neither of them moves when the scene is rotated.
Example: If you press [Winkel α] on this site https://www.swisseduc.ch/chemie/molekularium/proteine_op/mu_opioid/b/index.html, with newer versions of jsmol everything is correctly displayed except for the letters that appear shifted to the right. As the site runs with an older version, everything is still ok.
Thank you very much.
Urs
Please excuse, that was the wrong link, I meant:
https://www.swisseduc.ch/chemie/molekularium/tetraeder/tetraeder/b/index.html
Last edit: Urs Leisinger 2023-11-28
Confirmed: a PNGJ saved from Urs' webpage (JSmol 14.29.29) and dropped onto Jmol 16.1.47 shows the shift in all positions of echo.
Looks like when I added the PyMOL-style offset business I set the wrong default for that. It is positioning the labels to the right much too far. If you look in the state using
show state/echo
This will be fixed in the next version, and I will put a note in the Jmol.properties files about how this exactly works.
If you look at the state current Jmol writes, you will see that Jmol has set a default PyMOL offset of {-1 2 0 0 0 0 0 ]. The -1 is a mode marker, indicating that the next three numbers are horizontal, vertical, and depth offsets. "2" is indicating a two-angstrom offset to the right. It's probably not a great default. And your model is small enough to make it ridiculously large.
If you want those exactly like they were, I think you will have to add this:
set echo ID "e_a2" offset [-1 1.025 1 0 0 0 0 ]
set echo ID "w_a1" offset [-1 1.025 1 0 0 0 0 ]
set echo ID "e_c" offset [-1 1.025 1 0 0 0 0 ]
set echo ID "e_b1" offset [-1 1.025 1 0 0 0 0 ]
or, if you want something very close, you could use
set echo ID "e_a2" LEFT
which is the default it is supposed to be.
Or just hold on for the next release.
Bob