Manual for BioBlender 2.0

[zeffii]

i've seen videos and documentation for the custom Blender Buiild of BioBlender 0.5 (i think) ., but docs for the addon version is something i'm missing. Any links? Else we need to start generating docs

[MonZop]

There is a video that explains how to use BB2, but it is in italian, with italian subtitles. Also, it is centered on the new freatures that BB2 introduces relative tpo BB1, i.e. the handling of two or more molecules in the same scene. The video is quite big, 11 minutes and 115 MB!

[zeffii]

I found this neat useful poster you did in 2013 http://www.scivis.it/wp-content/uploads/2013/11/PosterECCB2010.pdf . It might be a good starting point for better documentation.

[MonZop]

The poster, other video and links to papers are all available at our website www.scivis.it/publications. Hoewever, they are all related to BB 0.6 or earlier, or to general principles of visualization and motion elaboration. For documenting BB2, I think Ican start doing something:

• general introduction to BB2 (relative to earlier versiones)
• Instruction manual for various features
• video tutorial? (I prefer pdf to video tutorial, but many people like video tut)

[MonZop]

Have you seen the Manual that Mike prepared for the 2.55 version of BioBlender? It is a pdf file (have been tryint g to upload, but don't know how)

[zeffii]

No, it might be handy!

[MonZop]

Manual outline

1. What is BioBlender
   • basic ideas on motion and visualization; why Blender,
   • BB2.0 structure (as in computer sc. Meaning)
2. Install
3. Import molecule
   • The pdb file
   • atoms and bonds
   • importing 2 or more molecules
4. Visualization
   • Atoms
   • Surface
   • MLP
   • EP
5. Motion
   • Moving molecules (cahnges of conformation)
     • Interpolation between conformations
     • Normal Mode Analisys
     • MD trajectory
   • Interacting molecules (moving relative to each other)
6. Make movies
7. Export data

[pmadhikar]

I am very interested in using BioBlender for visualizations. I couldn't find any instructions on getting started though. So a manual or even a simple tutorial would be very helpful. It wasn't clear to me what to do after I cloned this repo.

[zeffii]

Installation

(this text will change as BioBlender progresses into a more mature package).

At the end of both methods you should have a Folder named BioBlender located in your scripts folder.

path_to_your_scripts_folder \ scripts \ addons \ BioBlender

It is important for the functionality of the addon that this folder is called exactly BioBlender and not BioBlender-some_appendix. The content of the BioBlender folder will depend on which branch you checked out or downloaded as zip. It may look something like this:

Via Git

If you are familiar with git:

• clone the repo locally
• symlink its location on disk to scripts\addons\BioBlender [**].

Via Zip / Archive

At the moment avoid using the 'install from zip' feature in Blender > Preferences > Addons window.

• download the zip
• unpack it somewhere in a temporary location
• rename the innermost BioBlender-<branch_name> folder to BioBlender (it might be called BioBlender-master or -some_other_name)
• drop the innermost BioBlender folder into scripts\addons [**].

[**] Don't know where your scripts folder is? Enter bpy.utils.script_paths() into Blender's Python console. It will return a list of all locations on disk that this Blender.exe will look in for addons/scripts, any should do.

[zeffii]

Import Molecule

(this text is subject to change to reflect future developments)

from PDB

BioBlender ships with several test .pdb files, each of which hopes to show and test a capability of the addon.

To import a pdb

• go to the pdb import panel
• click the file browser
• navigate to Test_molecules
• select 06_1L2Y_4GE.pdb , then Accept
• press the make preview (this analyzes the pdb and displays some content information)
• press the big Import PDB button

Importing will take anywhere between 2 seconds and 2 minutes (or longer) depending on pdb complexity. During this time each Atom in the .pdb is rigged for simulating the Molecular dynamics

[zeffii]

@pmadhikar hopefully this will get you started.

[MonZop]

@pmadhikar I am preparing the manual; it is still incomplete, but it can help. I am not sure how to pass it , as a pdf file: any suggestion?

[zeffii]

send it to me I will push it to the master branch

[zeffii]

@MonZop @pmadhikar https://github.com/MonZop/BioBlender/blob/master/BB2%20Manual_WIP.pdf?raw=true one click to download

[zeffii]

@MonZop perhaps also the manual can be done from source / open, making it easy to edit for those with privileges. The wiki section of the github repo is quite a nice solution (may seem weird at first), and has markdown support to simplify formatting.

Converting from Wiki to PDF wouldn't be a big deal.

[pmadhikar]

@zeffii @MonZop This has helped me a lot. Thank you both. I will play around a little and ask more questions later. I think the wiki is a good idea. A lot of projects use that feature and it can be kept up to date easily.

[nantille]

I second the urgent need for an install guide as I tried things on my own but it seems BioBlender is half-running or I have no idea how to make it perform what I wish.

I have tried installing and using BioBlender and I'd like to give a feedback here. First I couldn't find a "Getting started" guide and that led me to some difficult times setting up BioBlender properly. Like I had no idea that some blend files were needed in the add-on directory. For when I install the plugin through the Blender UI, it only copies some python files, not the rest of the necessary assets.

Then I had to find videos about BioBlender that are several years old and the only feature I was looking for was the surface mesh representation of a molecule. I failed at finding how to do this with BioBlender.

For some reasons, BioBlender 0.6 doesn't work on Yosemite. It doesn't work either on Red hat 64 bit clusters that we have for it is specifically looking for 32bit libraries. So that rules the old version out.

So far I have a custom version of BioBlender that runs of my Yosemite machine but for the the life of me I couldn't find how to have a surface mesh representation of molecules.

I'll follow your guide and see if it works better.

[MonZop]

@nantille @pmadhikar The manual is being transferred to the wiki. In the meantime, please download from the link indicated above. @nantille

I had no idea that some blend files were needed in the add-on directoryy. For when I install the plugin through the Blender UI, it only copies some python files, not the rest of the necessary assets.

If you follow the installation instruction there should be no need for additional files. Make sure you have pyMOL in order to build the surface

[nantille]

I confirm that if I follow the guide (here with cloning git repo), the install works on Blender 2.73a on Mac Yosemite. Thank you.

[MonZop]

Good! Let us know if you have any further problems