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 <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.
>>
>>
>
>
> ------------------------------------------------------------------------------
> 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
------------------------------------------------------------------------------
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
