Visualize Bar ============= The visualize bar is divided into a few tabs: * Particles tab Controls the list of atoms / proteins / meshes. * Colors Controls the attributes and coloring of atoms. * Graphics Controls the options of realtime-rendering of the scene. * Render Controls the options of offline-rendering (image / video output). * Information Displays the math for the nerds, as well as additional information for selected atoms. Particles Tab ------------- The particles tab controls the drawing of atoms and proteins. .. image:: img/vpart.png ========================== ================== Button Function ========================== ================== |vexp| Expands / Collapses the group |vsela| Selects everything |vsel0| Deselects everything |vseli| Flip selection |vbal| Changes the draw mode (see ``Draw Modes``) of the group / selection |veye| Shows / Hides the group / selection ========================== ================== .. |vexp| image:: img/vexp.png .. |vsela| image:: img/vsela.png .. |vsel0| image:: img/vsel0.png .. |vseli| image:: img/vseli.png .. |vbal| image:: img/vbal.png .. |veye| image:: img/veye.png Atoms are grouped into Residues -> Residue ID -> atom name. .. TODO:: Add the protein section Attributes Tab -------------- Attributes ~~~~~~~~~~ Attributes are general data for each particle, optionally animated. A system can have an arbitary number of attributes. Attributes can be filled with the ``Set Attribute`` node, and queried with the ``Get Attribute`` node. .. image:: img/cattr.png Colors ~~~~~~~~ The colors section controls the color for atoms and bonds. .. image:: img/cols.png .. image:: img/grads.png * Bond colors ===================== ============== Option Details ===================== ============== Custom Bond Colors Use a custom color instead of atom colors Blend Bond Colors Blend colors inherited from atoms ===================== ============== Radii ~~~~~~~ ===================== ============== Option Details ===================== ============== Scale Multiply all radii values by this value ===================== ============== Bounding Box ~~~~~~~~~~~~~~~ ===================== ============== Option Details ===================== ============== Draw Draw the Box in 3D view Center X, Y, Z Box center coordinates Periodic Wrap around atoms outside the bounding box ===================== ============== Orientation ~~~~~~~~~~~ * Type ===================== ============== Type Details ===================== ============== Stretch Stretch atoms based on directions Vector Draw per-atom arrows toward directions ===================== ============== Graphics Tab ------------ The graphics tab controls the shading of the scene. * Shading .. image:: img/gshd.png ========= ============== Option Details ========= ============== Classic The scene is shaded with Lambert and Blinn-Phong lighting. Slightly faster but lower quality. PBR The scene is shaded with Environment Maps. Higher quality but slightly slower and uses more memory. ========= ============== * Lighting .. image:: img/glight.png ============ ============== Option Details ============ ============== Sky Environment type (backgrounds are in the backgrounds/ folder) Strength Strength of diffuse lighting (environment strength) Falloff How much the light gets weaker when further away from the camera Offset Falloff distance starts from this distance from the camera Specular The strength of reflection. For PBR, diffuse intensity = 1 - specular intensity Transparency Transparency ratio IOR Index of Refraction for transparency Background Background type: Color, Ambient, Sky Color Background color ============ ============== * Camera .. image:: img/gcam.png ===================== ============== Option Details ===================== ============== Follow Camera always centers on target Center X,Y,Z Camera axis Rotation W, Y Camera angle Scale Camera zoom factor Quality Resolution scaling of the scene Use Dynamic Quality Use a different resolution scale when moving the camera. Suitable for heavy scenes. Quality 2 Resolution scaling of the scene when the camera is moving ===================== ============== * Clipping .. image:: img/gclp.png ===================== ============== Option Details ===================== ============== None All atoms are shown Slice Only atoms in the bounding plane + thickness is shown Cube Only atoms in the bounding volume is shown ===================== ============== * Effects Additional effects to apply to the scene .. image:: img/geff.png List of effects available: * Glow ===================== ============== Option Details ===================== ============== Threshold Minimum brightness value Radius Blur radius Strength Additive strength ===================== ============== * Ambient Occlusion ===================== ============== Option Details ===================== ============== Samples Number of samples to average Radius Radius for sampling Strength Darken intensity Blur Blur radius before darkening ===================== ============== * Depth of Field ===================== ============== Option Details ===================== ============== Distance Focal distance from camera Aperture Blur amount Iterations Number of blur operations. Larger number is slower but reduces artifacts ===================== ============== Render Tab ---------- * To Image (GLSL) Produces a high resolution screenshot of the view. .. image:: img/rimg.png ===================== ============== Option Details ===================== ============== Width Width of the image (maximum 16k) Height Height of the image (maximum 16k) Slices Render in parts, improves render speed when the image resolution is very large MSAA Averages the final image over 4 samples. Slower but more beautiful. ===================== ============== * To Video (GLSL) Produces a high resolution screenshot video of the animation playback. .. image:: img/rmov.png ===================== ============== Option Details ===================== ============== Format Video format (GIF / AVI / PNG sequence) Width Width of the video (maximum 16k) Height Height of the video (maximum 16k) Slices Render in parts, improves render speed when the video resolution is very large MSAA Averages the final image over 4 samples. Slower but more beautiful. Max Frames Maximum frames to render. Snapshots will be skipped if there are too many frames. ===================== ==============