Re: [PyMOL] reproduce special vrml-output
Hi Thomas,
that's the trick, thank you so much, you saved me a ton of work!
Best,
Anke
Am 19.05.2017 um 13:15 schrieb Thomas Holder:
> Hi Anke,
>
> surface_type 0 will produce faces (solid triangles).
>
> There are no triangle faces in surface_type 2, only edges.
>
> Thomas
>
>> On May 19, 2017, at 12:43 PM, Anke Schultz
>> wrote:
>>
>> Hi Thomas,
>>
>> thanks for the explanation on adjusting view, it works fine. This leaves me
>> with one question: How do I get a .wrl-file containing only faces? Using
>> "show surface" and setting surface_type to 2 (triangles) gives me sticks and
>> spheres in the .wrl-file (sticks as edges, spheres at the ends of every
>> edge).
>>
>> Cheers,
>>
>> Anke
>>
>>
>> Am 19.05.2017 um 10:38 schrieb Thomas Holder:
>>> Hi Anke,
>>>
>>> The obvious difference I can see in your two samples is that the first one
>>> contains sticks and spheres representations, and the second one only has
>>> faces (could be surface or cartoon).
>>>
>>> The other difference is the viewport z position (zoom distance), which is
>>> 0.0 in the second sample. This can be set as follows before exporting the
>>> file (note that the molecule might not be visible anymore, it could be
>>> behind the camera):
>>>
>>> view = list(cmd.get_view())
>>> view[11] = 0.0
>>> cmd.set_view(view)
>>>
>>> Hope that helps.
>>>
>>> Cheers,
>>>Thomas
>>>
On May 17, 2017, at 4:27 PM, Anke Schultz
wrote:
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 0.00 0.979930 2.401556
children [
Shape {
geometry Cylinder {
radius 0.024352
height 0.139351
bottom FALSE
topFALSE
}
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 0.00 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.
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
Re: [PyMOL] reproduce special vrml-output
Hi Anke -
Try `as surface`, which is the equivalent of `hide everything; show surface`.
Hope that helps.
Cheers,
Jared
Sent from my iPhone
> On May 19, 2017, at 6:43 AM, Anke Schultz
> wrote:
>
> Hi Thomas,
>
> thanks for the explanation on adjusting view, it works fine. This leaves
> me with one question: How do I get a .wrl-file containing only faces?
> Using "show surface" and setting surface_type to 2 (triangles) gives me
> sticks and spheres in the .wrl-file (sticks as edges, spheres at the
> ends of every edge).
>
> Cheers,
>
> Anke
>
>
>> Am 19.05.2017 um 10:38 schrieb Thomas Holder:
>> Hi Anke,
>>
>> The obvious difference I can see in your two samples is that the first one
>> contains sticks and spheres representations, and the second one only has
>> faces (could be surface or cartoon).
>>
>> The other difference is the viewport z position (zoom distance), which is
>> 0.0 in the second sample. This can be set as follows before exporting the
>> file (note that the molecule might not be visible anymore, it could be
>> behind the camera):
>>
>> view = list(cmd.get_view())
>> view[11] = 0.0
>> cmd.set_view(view)
>>
>> Hope that helps.
>>
>> Cheers,
>> Thomas
>>
>>> On May 17, 2017, at 4:27 PM, Anke Schultz
>>> wrote:
>>>
>>> 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 0.00 0.979930 2.401556
>>> children [
>>> Shape {
>>>geometry Cylinder {
>>> radius 0.024352
>>> height 0.139351
>>> bottom FALSE
>>> topFALSE
>>>}
>>>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 0.00 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.
>>> 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,
>>> [...]
>>> ###
Re: [PyMOL] reproduce special vrml-output
Hi Thomas,
thanks for the explanation on adjusting view, it works fine. This leaves
me with one question: How do I get a .wrl-file containing only faces?
Using "show surface" and setting surface_type to 2 (triangles) gives me
sticks and spheres in the .wrl-file (sticks as edges, spheres at the
ends of every edge).
Cheers,
Anke
Am 19.05.2017 um 10:38 schrieb Thomas Holder:
> Hi Anke,
>
> The obvious difference I can see in your two samples is that the first one
> contains sticks and spheres representations, and the second one only has
> faces (could be surface or cartoon).
>
> The other difference is the viewport z position (zoom distance), which is 0.0
> in the second sample. This can be set as follows before exporting the file
> (note that the molecule might not be visible anymore, it could be behind the
> camera):
>
> view = list(cmd.get_view())
> view[11] = 0.0
> cmd.set_view(view)
>
> Hope that helps.
>
> Cheers,
>Thomas
>
>> On May 17, 2017, at 4:27 PM, Anke Schultz
>> wrote:
>>
>> 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 0.00 0.979930 2.401556
>> children [
>>Shape {
>> geometry Cylinder {
>> radius 0.024352
>> height 0.139351
>> bottom FALSE
>> topFALSE
>> }
>> 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 0.00 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.
>> 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
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
Re: [PyMOL] reproduce special vrml-output
Hi Anke,
surface_type 0 will produce faces (solid triangles).
There are no triangle faces in surface_type 2, only edges.
Thomas
> On May 19, 2017, at 12:43 PM, Anke Schultz
> wrote:
>
> Hi Thomas,
>
> thanks for the explanation on adjusting view, it works fine. This leaves me
> with one question: How do I get a .wrl-file containing only faces? Using
> "show surface" and setting surface_type to 2 (triangles) gives me sticks and
> spheres in the .wrl-file (sticks as edges, spheres at the ends of every edge).
>
> Cheers,
>
> Anke
>
>
> Am 19.05.2017 um 10:38 schrieb Thomas Holder:
>> Hi Anke,
>>
>> The obvious difference I can see in your two samples is that the first one
>> contains sticks and spheres representations, and the second one only has
>> faces (could be surface or cartoon).
>>
>> The other difference is the viewport z position (zoom distance), which is
>> 0.0 in the second sample. This can be set as follows before exporting the
>> file (note that the molecule might not be visible anymore, it could be
>> behind the camera):
>>
>> view = list(cmd.get_view())
>> view[11] = 0.0
>> cmd.set_view(view)
>>
>> Hope that helps.
>>
>> Cheers,
>> Thomas
>>
>>> On May 17, 2017, at 4:27 PM, Anke Schultz
>>> wrote:
>>>
>>> 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 0.00 0.979930 2.401556
>>> children [
>>> Shape {
>>>geometry Cylinder {
>>> radius 0.024352
>>> height 0.139351
>>> bottom FALSE
>>> topFALSE
>>>}
>>>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 0.00 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.
>>> 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 anyo
Re: [PyMOL] reproduce special vrml-output
Hi Anke,
The obvious difference I can see in your two samples is that the first one
contains sticks and spheres representations, and the second one only has faces
(could be surface or cartoon).
The other difference is the viewport z position (zoom distance), which is 0.0
in the second sample. This can be set as follows before exporting the file
(note that the molecule might not be visible anymore, it could be behind the
camera):
view = list(cmd.get_view())
view[11] = 0.0
cmd.set_view(view)
Hope that helps.
Cheers,
Thomas
> On May 17, 2017, at 4:27 PM, Anke Schultz
> wrote:
>
> 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 0.00 0.979930 2.401556
> children [
> Shape {
>geometry Cylinder {
> radius 0.024352
> height 0.139351
> bottom FALSE
> topFALSE
>}
>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 0.00 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.
> 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
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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[PyMOL] reproduce special vrml-output
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 0.00 0.979930 2.401556
children [
Shape {
geometry Cylinder {
radius 0.024352
height 0.139351
bottom FALSE
topFALSE
}
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 0.00 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.
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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