Hi all,
I've been experimenting with exporting surface meshes as .wrl-files. I
played with the geometry_export_mode setting and the set_view() options,
since I wanted to get the surface's coordinates corresponding to the
atom's coordinates of the sd-file I imported to pymol initially. I
realized that by exporting .wrl-format I got the camera-view instead of
the "real" coordinates as long as I left everything else on default.
This resulted in a shift between atom- and surface-coordinates.
While playing around to align camera and reality, I somehow managed to
change the way my .wrl-file looked in the end and it seems to be exactly
what I was looking for. I have tried for two days now, but unfortunately
I can't reproduce my steps leading to this special .wrl-file.
This is (part of) a .wrl-file without changing default settings:
###############################################################
/#VRML V2.0 utf8
Viewpoint {
position 0 0 20.39730644
orientation 1 0 0 0
description "Z view"
fieldOfView 0.465421
}
DirectionalLight {
direction -0.348155 -0.348155 -0.870
}
NavigationInfo {
headlight TRUE
type "EXAMINE"
}
Transform {
translation -1.820169 2.166291 -3.211221
rotation -0.199343 0.000000 0.979930 2.401556
children [
Shape {
geometry Cylinder {
radius 0.024352
height 0.139351
bottom FALSE
top FALSE
}
appearance Appearance {
material Material { diffuseColor 0.9000 0.9000 0.9000
specularColor 0.8 0.8 0.8
shininess 0.8 }
}
}
Transform {
translation 0.0 0.069676 0.0
children Shape {
geometry Sphere { radius 0.024352 }
appearance Appearance {
material Material { diffuseColor 0.9000 0.9000 0.9000
specularColor 0.8 0.8 0.8
shininess 0.8 }
}
}
}
Transform {
translation 0.0 -0.069676 0.0
children Shape {
geometry Sphere { radius 0.024352 }
appearance Appearance {
material Material { diffuseColor 0.9000 0.9000 0.9000
specularColor 0.8 0.8 0.8
shininess 0.8 }
}
}
}
]
}
Transform {
translation -1.906664 2.148911 -3.187284
rotation 0.635566 0.000000 0.772046 0.994256//
//[...]
###############################################################
/
And this is (part of) the special .wrl-file I mysteriously created:
/###############################################################
#VRML V2.0 utf8
Viewpoint {
position 0 0 -0.00000000
orientation 1 0 0 0
description "Z view"
fieldOfView 0.465421
}
DirectionalLight {
direction -0.348155 -0.348155 -0.870
}
NavigationInfo {
headlight TRUE
type "EXAMINE"
}
Shape {
appearance Appearance {
material Material { diffuseColor 1.0 1.0 1.0 }
}
geometry IndexedFaceSet {
coord Coordinate {
point [
1.121935 1.360173 -0.410155,
1.840800 1.307029 -0.904629,
1.445710 1.051540 -1.083943,
1.301289 0.550209 -1.380068,
1.445710 1.051540 -1.083943,
1.840800 1.307029 -0.904629,
2.165471 0.781700 -1.754629,
1.301289 0.550209 -1.380068,
1.840800 1.307029 -0.904629,
2.693056 1.515260 -1.343787,
2.165471 0.781700 -1.754629,
1.840800 1.307029 -0.904629,
[...]
###############################################################
/If anyone knows the way to this .wrl-format, I would really appreciate
your help./
/I'm using Pymol Version 1.8.6.0 on Ubuntu./
/
Thanks in advance,
Anke/
/
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