[Jmol-users] Jmol 12 issues

[Pshemak M. <pm...@ch...>]

  I am afraid that some things did not get resolved in the new versions. 
Below is the list.

PM

Run-times (approximate, from pressing "run" till surface is shown, all 
on the same desktop computer, no server involved)

isosurface peskin3 cutoff 0.05 resolution 3 phase color darkred darkblue 
atomicOrbital 3 1 0 1.0

12.1.8       4 s
12.0.10     4 s
12.0.8:      9 s
11.8.24:    2s (or less)

isosurface peskin3 cutoff 0.05 resolution 7 phase color darkred darkblue 
atomicOrbital 3 1 0 1.0

12.1.8       40 s
12.0.10     43 s
12.0.8:      100 s
11.8.24:    17s

All 12.xx are slower than 11.8.24, more than 2 times
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jvxl file reading not fixed in 12.0.10 and 12.1.8

Isosurfaces generated in 11.8.24 from smol (Spartan) file cannot be read 
in any of the 12 versions,. The molecular coordinates can be loaded if 
FILTER noOrient is used, attempts to load without filter, or attempts to 
load the isosurface freeze Jmol (12.0.8. 12.0.10, and 12.1.8)

Symptoms described previously (Bob, I e-mailed you the test file 
eplot11.jvxl).

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[set drawHover true]; isosurface escontour plane xy contour 30 
atomicOrbital 1 0 0 1.0

in.11.8.24 contour lines draw; can be read without set drawhover true  
[square bracket indicate that the script was run with and without that 
command]
in 12.0.8 works fine; contours can be read with set drawHover true (the 
values are slightly higher than those in 11.8.24)
in 12.0.10 and 12.1.8 three extra long triangles displayed and 
unfinished contour corners; contour values not shown with or without set 
drawHover true; contour in the center have different color than in the 
11.8.24 and 12.0.8

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[st drawHover true]; isosurface escross color absolute -0.01 0.9 plane 
xy resolution 6 atomicOrbital 1 0 0 1.0

in 11.8.24, circular color-filled contours produced with values read on 
color boundaries without set drawHover true
in 12.0.8  circular color contours produced with values read on contour 
boundaries only with set drawHover true; values slightly higher than 
those in 11.8.24
in 12.0.10 and 12.1.8 the largest contour is square, an there is a 
"hole" in the middle, the surface looks different, the values do not 
show with set drawHover