Re: [PyMOL] VRML export

[Sampson, Jared M.]

Hi Paul - I'm not too familiar with 3D printing, so not sure if this will help 
you or not.  But if all you need is to have extra cylinders in your output wrl 
file, you could add them using either CGO or distance objects directly within 
PyMOL.

https://pymolwiki.org/index.php/Distance
https://pymolwiki.org/index.php/CGOCylinder

Cheers,
Jared



On Sep 23, 2016, at 4:18 PM, Paul Paukstelis 
> wrote:

Thanks, Jared.

I did ultimately find it there. Looks like what I was shooting for isn't likely 
to be very straightforward. From what I can tell, it doesn't seem that any of 
the atom information gets passed into RayRender.

--p

On 09/23/2016 12:34 PM, Sampson, Jared M. wrote:
Hi Paul -

The relevant function used for VRML export is RayRenderVRML2() in 
layer1/Ray.cpp.

Cheers,

Jared

On Sep 22, 2016, at 11:43 AM, Paul Paukstelis 
> wrote:

Greetings,

I've started playing with 3D printing some ball-and-stick models
(primarily nucleic acids). I've worked up some Blender scripts to enable
automatic pinning (e.g. add a small pin to cylinder of the O3'-P bond
and a correspond hole in the phosphate sphere), however, I'm trying to
further decrease the amount of user input needed in Blender to
ultimately export the model parts for printing. One thing that would be
really useful would be to define some custom child nodes in the VRML
output (atom names for example) and subsequently input that into Blender
as custom properties. Could someone point me to the most relevant pymol
files responsible for VRML output? I did some quick fgrep'ing and didn't
find too much that was of use. Blender side was pretty easy to
accomplish so far.

Thanks,

--paul

--
___
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


--
___
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

Re: [PyMOL] VRML export

[Paul Paukstelis]

Thanks, Jared.

I did ultimately find it there. Looks like what I was shooting for isn't 
likely to be very straightforward. From what I can tell, it doesn't seem 
that any of the atom information gets passed into RayRender.

--p

On 09/23/2016 12:34 PM, Sampson, Jared M. wrote:
> Hi Paul -
>
> The relevant function used for VRML export is RayRenderVRML2() in 
> layer1/Ray.cpp.
>
> Cheers,
>
> Jared
>
>> On Sep 22, 2016, at 11:43 AM, Paul Paukstelis  
>> wrote:
>>
>> Greetings,
>>
>> I've started playing with 3D printing some ball-and-stick models
>> (primarily nucleic acids). I've worked up some Blender scripts to enable
>> automatic pinning (e.g. add a small pin to cylinder of the O3'-P bond
>> and a correspond hole in the phosphate sphere), however, I'm trying to
>> further decrease the amount of user input needed in Blender to
>> ultimately export the model parts for printing. One thing that would be
>> really useful would be to define some custom child nodes in the VRML
>> output (atom names for example) and subsequently input that into Blender
>> as custom properties. Could someone point me to the most relevant pymol
>> files responsible for VRML output? I did some quick fgrep'ing and didn't
>> find too much that was of use. Blender side was pretty easy to
>> accomplish so far.
>>
>> Thanks,
>>
>> --paul
>>
>> --
>> ___
>> 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


--
___
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

Re: [PyMOL] VRML export

[Sampson, Jared M.]

Hi Paul - 

The relevant function used for VRML export is RayRenderVRML2() in 
layer1/Ray.cpp.

Cheers,

Jared

> On Sep 22, 2016, at 11:43 AM, Paul Paukstelis  
> wrote:
> 
> Greetings,
> 
> I've started playing with 3D printing some ball-and-stick models 
> (primarily nucleic acids). I've worked up some Blender scripts to enable 
> automatic pinning (e.g. add a small pin to cylinder of the O3'-P bond 
> and a correspond hole in the phosphate sphere), however, I'm trying to 
> further decrease the amount of user input needed in Blender to 
> ultimately export the model parts for printing. One thing that would be 
> really useful would be to define some custom child nodes in the VRML 
> output (atom names for example) and subsequently input that into Blender 
> as custom properties. Could someone point me to the most relevant pymol 
> files responsible for VRML output? I did some quick fgrep'ing and didn't 
> find too much that was of use. Blender side was pretty easy to 
> accomplish so far.
> 
> Thanks,
> 
> --paul
> 
> --
> ___
> 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


--
___
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

[PyMOL] VRML export

[Paul Paukstelis]

Greetings,

I've started playing with 3D printing some ball-and-stick models 
(primarily nucleic acids). I've worked up some Blender scripts to enable 
automatic pinning (e.g. add a small pin to cylinder of the O3'-P bond 
and a correspond hole in the phosphate sphere), however, I'm trying to 
further decrease the amount of user input needed in Blender to 
ultimately export the model parts for printing. One thing that would be 
really useful would be to define some custom child nodes in the VRML 
output (atom names for example) and subsequently input that into Blender 
as custom properties. Could someone point me to the most relevant pymol 
files responsible for VRML output? I did some quick fgrep'ing and didn't 
find too much that was of use. Blender side was pretty easy to 
accomplish so far.

Thanks,

--paul

--
___
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

[PyMOL] vrml export normals

[aaron bryden]

Has anyone had good luck with the VRML export. It seems that there is
a problem with the normals that are exported in some cases.  Can
anyone recommend a VRML viewer that works well with the exported
files.

aaron

Re: [PyMOL] vrml export normals

[DeLano Scientific]

Just FYI -- use the latest open-source code or recent beta builds for
current VRML export, since older versions export faulty VRML.

Cheers,
Warren

 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net 
 [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
 Of aaron bryden
 Sent: Wednesday, April 18, 2007 12:15 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] vrml export normals
 
 Has anyone had good luck with the VRML export. It seems that 
 there is a problem with the normals that are exported in some 
 cases.  Can anyone recommend a VRML viewer that works well 
 with the exported files.
 
 aaron
 
 --
 ---
 This SF.net email is sponsored by DB2 Express Download DB2 
 Express C - the FREE version of DB2 express and take control 
 of your XML. No limits. Just data. Click to get it now.
 http://sourceforge.net/powerbar/db2/
 ___
 PyMOL-users mailing list
 PyMOL-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/pymol-users