Community:Science/Biology/StructuralBiology/BioBlender
BioBlender
(page under construction, Nov. 2011)
BioBlender is made and maintained by SciVis, in Pisa Italy. The dedicated website, for specific comments, blogs, news tutorial etc, is http://www.bioblender.eu
BioBlender contains a set of functionalities aimed at two tasks in handling atomic data: elaboration of motion and surface visualization, using a specific visual code. For both tasks, the basis is a pdb file
The starting material is ALWAYS a pdb file (or a file written in .pdb format, with atoms, atoms type, their 3D coordinates all nicely formatted). The first thing to do is select it: in the field BioBlender Import type the 4 letter code of a pdb to be fetched from the Protein Data Bank, or the path to your file, or press the folder icon to open a file browser.
BioBlender reads the file and report its contents:
the number of chains, typically 1, (or more for a complex solved by X-ray), and called A, B, C or sometimes a more meaningful letter
the number of MODELS: 1 for X-ray and typically between 10 and 50 for NMR files.
Note
if the file is not formatted according to the pdb specifications, BioBlender will not work
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Before importing, select which models and their order, set the Number of frames that Blender will use to interpolate in the Keyframe interval, check the options necessary for your work, and press Import pdb
If you imported more than one .pdb file, BioBlender will upload them, and directly interpolate each atom between the conformations. However, if the option Makebonds was checked, BioBlender can use the game engine and make a better interpolation, by pressing Run in game engine.
By selecting Collisions 1, Blender GE will calculate the movement considering: - The direction of the motion (linear, set in the IPO) - The collision factor - The rigid body joint, that allows only to rotate atoms along their bond axis
Note
For movement of better quality set a long keyframe interval (100 frames or more)
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By selecting Collisions 2, all frames calculated by the GE will be recorded, look 200 frames downstream from the frame of your last conformation.
Now you have all atoms keyframed, and can use this data to: Export data (set your preferences and the path to save the new pdb files), or use them for the visualization, using the BioBlender visual code.
For the MLP visualization choose a Formula, set the Grid spacing (expressed in Å) and press Show mlp on surface. MLP is calculated in every point of a grid in the protein space and visualized on the surface of the protein as grey levels (light areas for hydrophobic and dark areas for hydrophilic).
Contrast and Brightness sliders can be used to enhance the visualization of MLP. Once the representation is satisfactory, press Render mlp to surfacefor a photo-realistic rendering and press F12 to render it. Our novel code for the representation of MLP is a range of optical features that goes from shiny-smooth surfaces for hydrophobic areas to dull-rough surfaces for hydrophilic ones.
For the EP visualization choose a Formula, set the Ion concentration, the Grid spacing (expressed in Å), the Minimum potential (the minimum value for which the field lines are calculated), the N ep lines*ev/å² (the number of field lines calculated for eV/Ų) and press Show ep. EP is calculated using external programs and visualized as small particles flowing along the field lines (NURBS curves in Blender) from the positive to the negative end. If you want to change a setting and re-calculate EP, Clear ep and follow the previous steps.
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