- VMD CITATION MOVIE
- VMD CITATION SERIES
The sphere scale can be adjusted to make the atoms take up more or less space.
CPK - This creates a ball-and-stick drawing for atomistic models and isolated spheres for coarse-grain models. It's very fast, so for large systems (like 100,000+ atoms) this is the only real way of moving the viewpoint around without significant lag. Lines - Typically the default setup, this treats atoms and points and draws lines between them. There are many drawing method options, which can be mixed and matched to achieve the desired final result. The final major component of a representation is to decide how the atoms you've selected will be displayed. Example: segname ANTB or segname ANTG and ( not hydrogen or not resname HOH )Īdditional selection keywords, many of which are suited toward biological molecules, can be found in the Selections tab next to Draw Style. ( or ) - allows the user to group selections together. Example: not hydrogen, segname 1BDD and not sidechain. not - prevents atoms with the specified properties from being part of the selection. or - allows atoms with different properties to be in the selection. and - atoms must have all specified properties to be in the selection. Keywords and their selections can be combined using ( and boolean operators: To select all water molecules: resname HOH. To select all cysteine amino acids: resname CYS. resname - selects all molecule groups with a given name, such as amino acids, nucleic acids, or water molecules. name - selects an atom type, such as alpha-carbons, amine hydrogens, etc. To select a group of nonsequential atoms: index 389 or index 712 or index 954 or index. To select a group of sequential atoms: index 115 to 768. index - base 0, this allows the user to select single atoms or a group of atoms (and yes, the base 0 will mess with your brain endlessly.). To select multiple chains: chain A or chain C or chain E. chain - for protein and DNA structures selecting atoms by chain can be simple and useful, like using the segname selection. Selections don't have to be 4 letters long, example: segname FAB. segname - PDB, PSF, and CRD files can contain 4-letter segment identifiers that can be used to select groups of atoms. Graphics > Colors then selecting the "Display" option then selecting "Background" - Allows the user the change the background color. This can be used to make a "surface" on which surface-bound molecules can be placed so they're not just floating in space. Dispaly > Stage - Draws a stage on a specified part of the VMD Display window. For publication quality images this should be turned off, but it can help diagnose simulation problems when simulations involve a planar surface at z = 0. Dispaly > Axes - Allows the user to enable/move the position of the x, y, z arrows on screen. 
Again, it doesn't produce a nice image, so typically you will uncheck this option.
Display > Depth Cueing - Enables a "fog" that makes parts of the molecule further away from the camera appear washed out or darker. Orthographic instead renders the molecule as if it were something small enough to sit on your desk. With perspective enabled (as it must be if a stage is turned on) the viewer sees the molecule as if it were some ginormous thing that would fade to a single point in the distance. Display > Perspective vs Orthographic - This radial button defaults to perspective, but orthographic provides a better image overall. The coordinates of a loaded PDB file will count as a frame 0, so remember this if you load an additional trajectory file and need to extract data from a specific frame in that file or reference that frame later on.įor most simulation images there are a couple of changes to the default VMD display settings that yield a better looking image. VMD CITATION MOVIE
Please note that movie trajectories start at frame 0.
VMD CITATION SERIES
Multiple trajectory files can be loaded in series to produce a longer movie.
"Load all at once" tells VMD to silently load the trajectory data into RAM all at once. For large files do not do this as it will take a very long time. "Load in background" tells VMD to read the trajectory frame-by-frame and to draw each frame after loading. This takes the user back to the Molecule File Browser where the user has the option of telling VMD which frames from the trajectory file they wish to load and how they want them loaded. The user then finds and selects the desired trajectory file and clicks open. 
To do so, the user selects the molecule in the VMD Main window, right-clicks and selects Load Data into Molecule. For example, if a PDB was loaded, the user can then add TRR, DCD, or lammps_traj data to the molecule to view molecular motions. Once a molecular system has been set up, additional coordinate information can be added to it.
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