BioBlender 0.6 with NMA

An open space where people who use Blender in an academic environment can share progress and the typical problems and needs of academic environments.

Moderators: jesterKing, stiv

MonZop
Posts: 25
Joined: Wed Dec 16, 2009 9:51 am
Location: Pisa

BioBlender 0.6 with NMA

Postby MonZop » Mon Nov 14, 2011 2:58 pm

New release of BioBlender: v 0.6, made in collaboration with Nicolas Ferèy who integrated the calculation of proteins trajectories using Normal Mode Analysis. Please visit the BioBlender website to download for Linux, Windows and MacOS

PAleksandrov
Posts: 2
Joined: Fri Jun 29, 2012 1:15 pm

Re: BioBlender 0.6 with NMA

Postby PAleksandrov » Fri Jun 29, 2012 10:50 pm

MonZop wrote:New release of BioBlender: v 0.6, made in collaboration with Nicolas Ferèy who integrated the calculation of proteins trajectories using Normal Mode Analysis. Please visit the BioBlender website to download for Linux, Windows and MacOS

Is BioBlender fully open-source? Where can the sources for the last version be downloaded?

MonZop
Posts: 25
Joined: Wed Dec 16, 2009 9:51 am
Location: Pisa

Postby MonZop » Mon Jul 09, 2012 9:52 am

Completely open Source, yes!

Find all info and material at www.BioBlender.net

PAleksandrov
Posts: 2
Joined: Fri Jun 29, 2012 1:15 pm

Postby PAleksandrov » Sun Jul 15, 2012 1:11 pm

MonZop wrote:Completely open Source, yes!

Find all info and material at www.BioBlender.net

I have found only sources for BioBlender 0.5.1 (and, maybe, previous versions). But I haven't found sources for BioBlender 0.6. Is it the original blender version with python plugins (so the C++ code is not modified)?

bollili
Posts: 2
Joined: Wed Jul 18, 2012 8:40 pm

Postby bollili » Wed Jul 18, 2012 9:08 pm

Hey there,

I am a blender newbie, but quite experienced with other packages, though. I am using bioblender 0.6 (64 Bit, Win7)

I want to export scenes imported into bioblender as fbx or any other generic 3D format (MDD, Collada, ...) to get it into some other software.

The only thing I could get exported via fbx was the animated scene without any coloring and only as polygon spheres.

So got many questions, but this one is the most important for me:
How can I export an animated scene with the coloring and other attributes intact?

Cheers
Marc

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Wed Jul 25, 2012 3:15 pm

PAleksandrov wrote:
MonZop wrote:Completely open Source, yes!

Find all info and material at www.BioBlender.net

I have found only sources for BioBlender 0.5.1 (and, maybe, previous versions). But I haven't found sources for BioBlender 0.6. Is it the original blender version with python plugins (so the C++ code is not modified)?


Hi PAleksandrov!
As you said, Bioblender is the original Blender version with python plugins, the same as 0.5.1.
:)

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Wed Jul 25, 2012 3:22 pm

bollili wrote:Hey there,

I am a blender newbie, but quite experienced with other packages, though. I am using bioblender 0.6 (64 Bit, Win7)

I want to export scenes imported into bioblender as fbx or any other generic 3D format (MDD, Collada, ...) to get it into some other software.

The only thing I could get exported via fbx was the animated scene without any coloring and only as polygon spheres.

So got many questions, but this one is the most important for me:
How can I export an animated scene with the coloring and other attributes intact?

Cheers
Marc


Hi Marc!
For fbx files, i doubt the animation can be saved.
Collada should work. See here
http://wiki.blender.org/index.php/Doc:2 ... rt/COLLADA
If you still have trouble to export the geometry, try to save the animated scene, reopen it in the newest version of Blender and export from there.
That has probably a more complete and updated set of export plugins.
:)

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Wed Jul 25, 2012 3:38 pm

TiZeta wrote:
bollili wrote:Hey there,

I am a blender newbie, but quite experienced with other packages, though. I am using bioblender 0.6 (64 Bit, Win7)

I want to export scenes imported into bioblender as fbx or any other generic 3D format (MDD, Collada, ...) to get it into some other software.

The only thing I could get exported via fbx was the animated scene without any coloring and only as polygon spheres.

So got many questions, but this one is the most important for me:
How can I export an animated scene with the coloring and other attributes intact?

Cheers
Marc


Hi Marc!
For fbx files, i doubt the animation can be saved.
Collada should work. See here
http://wiki.blender.org/index.php/Doc:2 ... rt/COLLADA
If you still have trouble to export the geometry, try to save the animated scene, reopen it in the newest version of Blender and export from there.
That has probably a more complete and updated set of export plugins.


Sorry, my mistake...
Fbx shoul work too, in newest version.
http://wiki.blender.org/index.php/Exten ... Py/Scripts
You can find the complete list of export scripts and their charateristics here:
http://wiki.blender.org/index.php/Exten ... Py/Scripts
:)

bollili
Posts: 2
Joined: Wed Jul 18, 2012 8:40 pm

Postby bollili » Wed Jul 25, 2012 3:58 pm

Hi TiZeta,

it's so obvious! :D

Thanks, opening the blend-file with blender 2.63 worked great. And the fbx export is perfect. You made me very happy. :)

Question 1:
But, the atoms are represented as simple spheres, only.
If I want to export the whole animation as a surface, what would I have to do?
Right now, I can just generate a surface for the actual frame only via "Show EP". So it isn't animated anymore. :(

Question 2:
The buttons "Show MLP on Surface" and "Calculate NMA trajectories (pdb)" don't work for me. They alway throw an error (Error 87 "Wrong Parameter"). I use the supplied demo scenes but also tried other files - same problem.

Thanks for your help!

Cheers

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Thu Jul 26, 2012 12:43 pm

bollili wrote:Hi TiZeta,

it's so obvious! :D

Thanks, opening the blend-file with blender 2.63 worked great. And the fbx export is perfect. You made me very happy. :)

Question 1:
But, the atoms are represented as simple spheres, only.
If I want to export the whole animation as a surface, what would I have to do?
Right now, I can just generate a surface for the actual frame only via "Show EP". So it isn't animated anymore. :(

Question 2:
The buttons "Show MLP on Surface" and "Calculate NMA trajectories (pdb)" don't work for me. They alway throw an error (Error 87 "Wrong Parameter"). I use the supplied demo scenes but also tried other files - same problem.

Thanks for your help!

Cheers


For the first question, unfortunately the surface is not animatable at the moment, but the feature is planned for the future.
:)


Return to “Academic & Research”

Who is online

Users browsing this forum: No registered users and 0 guests