Dear Bob, Dear Jmol developers and users, I'm trying to use Jmol for representing in a realistic manner the angles that describe the arrangement of atoms around a given centre. These angles are sketched in the attached figure "model.png".
While doing this, with Jmol-11.5.26, I've found two bugs.
1) PovRay rendering of "circles" is buggy: circles are
displayed as filled cylinders.
- render_view.simple.jpg: this file as been obtained by
using the "save current view as a image" button -> fine
- render_view.povray.png: the PovRay rendering of the
same view: you can notice the dark thin cylinders.
The view can be reproduced with the attached files:
"main.xyz" and "script_part1"
2) The WIDTH and OFFSET options of the DRAW command
show unexpected (buggy ?) behaviour.
This can be notice with the attached file "script_part2".
It contains the commands which I'm trying to use to sketch
the angles.
- Drawing 'cone1_generator' with a 'WIDTH' smaller than
0.05 gives strange results. The OFFSET option doesn't
seem to be working.
- The segments 'angle1_a' and 'angle1_b' are not correctly
drawn unless a 'WIDTH' of 0.05, at least, is used to draw
them.
Please don't hesitate to contact me for any further information.
Best regards,
Max
--
***********************************************
Latevi Max LAWSON DAKU
Departement de chimie physique
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet
CH-1211 Geneve 4
Switzerland
Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103 ***********************************************
<<inline: model.png>>
main.xyz
Description: Xmol XYZ data
# let's draw the main frame
# --
load "main.xyz"
color background white
restrict not selected;select not selected;spacefill 12%;wireframe 0
color cpk
hide (carbon)
# draw fe_n_1 (atomno=1) (atomno=2) width 0.02 color black
# draw fe_n_2 (atomno=1) (atomno=3) width 0.02 color black
# draw fe_n_3 (atomno=1) (atomno=6) width 0.02 color black
# draw fe_n_4 (atomno=1) (atomno=7) width 0.02 color black
# draw fe_n_5 (atomno=1) (atomno=10) width 0.02 color black
# draw fe_n_6 (atomno=1) (atomno=11) width 0.02 color black
draw n_c_1 (atomno=2) (atomno=4) width 0.05 color black
draw c_c_1 (atomno=4) (atomno=5) width 0.05 color black
draw c_n_1 (atomno=5) (atomno=3) width 0.05 color black
draw n_c_2 (atomno=6) (atomno=8) width 0.05 color black
draw c_c_2 (atomno=8) (atomno=9) width 0.05 color black
draw c_n_2 (atomno=9) (atomno=7) width 0.05 color black
draw n_c_3 (atomno=10) (atomno=12) width 0.05 color black
draw c_c_3 (atomno=12) (atomno=13) width 0.05 color black
draw c_n_3 (atomno=13) (atomno=11) width 0.05 color black
# let's draw the trigonal axis
# --
set axes on
set axesmolecular
rotate x 90 molecular
rotate z 30 molecular
draw arrow1 arrow width 0.04 color [160,180,180] {0 0 3.5} {0 0 -3.5}
set axes off
# let's represent the planes that help define the torsion angle \gamma
# --
draw plane1 plane (atomno=10) (atomno=12) (atomno=13) (atomno=10)
color $plane1 [180,180,180] translucent
draw plane2 plane (atomno=12) (atomno=13) (atomno=11) (atomno=12)
color $plane2 [180,180,180] translucent
# let's draw the circles associated with the N and N' atoms
# --
x1 = {atomno=2}.X
y1 = {atomno=2}.Y
z1 = {atomno=2}.Z
circle1_radius = {atomno=2}.distance({0,0,@z1})
pt_a = point(0,0,@z1)
pt_b = point(0,0,@{z1+0.02})
draw circle1 width @{circle1_radius*2} @pt_a @pt_b mesh nofill color black
x2 = {atomno=3}.X
y2 = {atomno=3}.Y
z2 = {atomno=3}.Z
circle2_radius = {atomno=3}.distance({0,0,@z2})
pt_a = point(0,0,@z2)
pt_b = point(0,0,@{z2-0.02})
draw circle2 width @{circle2_radius*2} @pt_a @pt_b mesh nofill color black
# let's draw the triangles used to define twist angle
# --
cos120 = -0.5
sin120 = 0.8660254
z_plane= 5.0
triangle1_1 = point([EMAIL PROTECTED] @y1 @z_plane})
x_tmp1 = cos120*x1+sin120*y1
y_tmp1 = -sin120*x1+cos120*y1
triangle1_2 = point([EMAIL PROTECTED] @y_tmp1 @z_plane})
x_tmp2 = cos120*x_tmp1+sin120*y_tmp1
y_tmp2 = -sin120*x_tmp1+cos120*y_tmp1
triangle1_3 = point([EMAIL PROTECTED] @y_tmp2 @z_plane})
draw triangle1_segment1 @triangle1_1 @triangle1_2 width 0.05 color black
draw triangle1_segment2 @triangle1_2 @triangle1_3 width 0.05 color black
draw triangle1_segment3 @triangle1_3 @triangle1_1 width 0.05 color black
draw triangle1_surface vertices @triangle1_1 @triangle1_2 @triangle1_3
color $triangle1_surface translucent [200,200,200]
triangle2_1 = point([EMAIL PROTECTED] @y2 @z_plane})
x_tmp1 = cos120*x2+sin120*y2
y_tmp1 = -sin120*x2+cos120*y2
triangle2_2 = point([EMAIL PROTECTED] @y_tmp1 @z_plane})
x_tmp2 = cos120*x_tmp1+sin120*y_tmp1
y_tmp2 = -sin120*x_tmp1+cos120*y_tmp1
triangle2_3 = point([EMAIL PROTECTED] @y_tmp2 @z_plane})
draw triangle2_segment1 @triangle2_1 @triangle2_2 width 0.05 color black
draw triangle2_segment2 @triangle2_2 @triangle2_3 width 0.05 color black
draw triangle2_segment3 @triangle2_3 @triangle2_1 width 0.05 color black
draw triangle2_surface vertices @triangle2_1 @triangle2_2 @triangle2_3
color $triangle2_surface translucent [200,200,200]
# let's sketch the cone angles \theta and \theta^\prime
# --
cos045 = 0.70710678 # cos(45)
sin045 = 0.70710678 # sin(45)
pt_c1 = point([EMAIL PROTECTED] @{-sin045*x1+cos045*y1} @z1})
displ1 = (pt_c1/pt_c1)*0.250
draw cone1_generator scale 1.2 {0 0 0} @pt_c1 width 0.05 offset @displ1
color $cone1_generator black
# let's sketch the twist angle \tau
# --
draw angle1_a scale 1.75 @triangle1_1 @triangle1_2 width 0.03
color $angle1_a [200,200,200]
draw angle1_b scale 1.75 @triangle2_1 @triangle2_2 width 0.03
color $angle1_b [200,200,200]
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