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<tr><td><b>HELP! : </b> Fellow Blenderheads please help improve this page!!!</td></tr>
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== Introduction ==
== Introduction ==
An attempt at using Blender, an open-source, free, 3D modeling software to render, pose and animate objects exported from Pymol.
This is an attempt at using [https://en.wikipedia.org/wiki/Blender_(software) Blender], an open-source, free, 3D modeling software to render, pose and animate objects exported from Pymol.


Blender may be downloaded freely for all major platforms (Win/Mac/Linux), from: http://www.blender.org/download/get-blender/
Blender may be downloaded freely for all major platforms (Win/Mac/Linux), from: http://www.blender.org/download/get-blender/


A great starting place for getting comfortable with Blender is the Blender Wiki: http://wiki.blender.org/
These tutorials are for Windows.


== Examples ==
== Tutorials ==
Representative examples. Please change/improve.
Representative examples. Please change/improve.


=== 1. Translucent Surfaces ===
=== [[1. Importing a PyMol Structure into Blender]] ===
 
=== [[2. Translucent Surfaces]] ===
High quality translucent surfaces, better than PyMOL's internal renderer/ray-tracer.
High quality translucent surfaces, better than PyMOL's internal renderer/ray-tracer.


* '''Step 1'''
=== [[3. Joining Atoms]] ===
Load the PDB file 3IQS into PyMOL, duplicate it twice and rename the two new objects to "3IQS_cartoon" and "3IQS_surface" as shown in the image below:
 
[[Image:Scr01.png|center|350px]]
 
* '''Step 2'''
Turn off the display of "3IQS_surface" as shown below:
 
[[Image:Scr02.png|center|350px]]
 
* '''Step 3'''
Save the displayed "3IQS_cartoon" as a VRML file, as shown below:
 
[[Image:Scr03.png|center|350px]]
 
* '''Step 4'''
Hide the "3IQS_cartoon" and display the "3IQS_surface". Again, save the displayed "3IQS_surface" as a VRML file, as shown below:
 
[[Image:Scr04.png|center|350px]]
 
* '''Step 5'''
Start Blender (please see link in the Introduction to download and install). Assuming you are looking at the default scene and window layout, press '''7''' on '''numeric keypad''' and the view should change similar to the one below:
 
[[Image:Scr05.png|center|350px]]
 
Now select the '''cube''' in the center of the screen by '''right clicking''' on it and then press '''ctrl-x''' to delete it. This will give you a clean scene to import the protein structure you just exported from PyMOL as VRML 2 (.wrl).
 
* '''Step 6'''
Now import the "3IQS_cartoon" into Blender by going to "File > Import > X3D & VRML97" as shown below:
 
[[Image:Scr06.png|center|350px]]
 
* '''Step 7'''
Navigate to the folder where you exported the VRML 2 files from PyMOL and select the "3IQS_cartoon" file, thusly:
 
[[Image:Scr07.png|center|350px]]
 
Click the "Import X3D/VRML97" button after selecting the correct file and just click "OK" on the dialog that comes up.
 
* '''Step 8'''
Doing the above should result in a display such as the one below:
 
[[Image:Scr08.png|center|350px]]
 
* '''Step 9'''
Now you need to select the just imported cartoon and just that only, so '''right click''' on it so that it is the only object selected in the view:
 
[[Image:Scr09.png|center|350px]]
 
* '''Step 10'''
With the cartoon object selected, hit the '''Tab'' key on your keyboard to enter into "Edit mode" in Blender. All the vertices  that make up this object will be selected and colored yellow, as shown below:
 
[[Image:Scr10.png|center|350px]]
 
* '''Step 11'''
Now click on "Mesh > Vertices > Remove Doubles" in Blender to get rid of duplicate vertices, as shown in the two images below:


[[Image:Scr11.png|center|350px]]
== Why Blender? ==
[[Image:Scr12.png|center|350px]]


* '''Step 12'''
* Blender is FREE (as in beer)
Now hit the '''Tab'' key again, to exit the "Edit mode" to see a nice smooth cartoon object:
* Blender is Open Source and therefore FREE (as in freedom)
* Blender is an extremely capable 3D graphics program and perhaps the only FOSS program capable of taking on similar commercial software head-to-head (Maya/Max/Modo etc.)
* To see some examples of what Blender can do check out:
** http://www.elephantsdream.org/
** http://www.bigbuckbunny.org/
** http://www.yofrankie.org/


[[Image:Scr13.png|center|350px]]
== Blender Help ==
Blender is a perfect complement to PyMOL for creating high quality images and animation, but has a pretty steep learning curve. The following are a few resources that may be of help along the way:


* '''Step 13'''
* http://www.blender.org/education-help/
* http://en.wikibooks.org/wiki/Blender_3D:_Noob_to_Pro/Beginner_Tutorials
* http://forums.cgsociety.org/forumdisplay.php?f=91
* http://blenderartists.org/forum/


== References ==
== References ==
* Blender : http://www.blender.org/
* Blender : http://www.blender.org/

Latest revision as of 00:48, 25 October 2014

HELP! : Fellow Blenderheads please help improve this page!!!

Introduction

This is an attempt at using Blender, an open-source, free, 3D modeling software to render, pose and animate objects exported from Pymol.

Blender may be downloaded freely for all major platforms (Win/Mac/Linux), from: http://www.blender.org/download/get-blender/

A great starting place for getting comfortable with Blender is the Blender Wiki: http://wiki.blender.org/

These tutorials are for Windows.

Tutorials

Representative examples. Please change/improve.

1. Importing a PyMol Structure into Blender

2. Translucent Surfaces

High quality translucent surfaces, better than PyMOL's internal renderer/ray-tracer.

3. Joining Atoms

Why Blender?

Blender Help

Blender is a perfect complement to PyMOL for creating high quality images and animation, but has a pretty steep learning curve. The following are a few resources that may be of help along the way:

References

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