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 <anke.schu...@tu-braunschweig.de>
>> 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
>>>> <anke.schu...@tu-braunschweig.de> 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 0.000000 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
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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