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.
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
