yob file and can be broken into smaller pieces. A Mol can be as simple as a single atom or a single amino acid or be larger and composed of several atoms or amino acids. Mol (Molecule) – A Mol is the second level of organization and typically refers to a single contiguous chain within the scene. Objects can be split into several objects. An object is a complete model composed of one or more molecules. Obj (Objects) – Objs are the highest level of organization. Let’s unpack each level in a bit more detail before showing how this might be useful. In the simplest sense, an Object consists of one or more Mol (Molecules) which consists of one or more Res (Residues) which consist of one or more Atoms. YASARA organizes models at several levels, which permits easier control of manipulations to the model. 10.6 Menu bar or Continue Button does not respond to clicksģ.4 What does Obj vs. Mol vs. Res vs. Atom mean?.10.4 MacOS won’t allow YASARA to run because not from App Store.9.5.1 Data Management Plan questions for students in Biochemistry class:.9.3.1 Information to consider including in file names.7.3.1 Commands that can be used in a macro.7.2.1 The # as a way to help your reader (and you!).6.7 Making amino acid or nucleotide substitutions.6.6.1 Why did my Obj/Mol move (or not)?.5.4.1 Considerations when making a biomolecule figure.4.3.2 Color by Element and other features.4.2.2 Showing and Hiding Atoms and Amino Acids.4.1 Positioning and orienting the model.3.4.1 Why is the organization important?.3.4 What does Obj vs. Mol vs. Res vs. Atom mean?.3.2 Starting to work with models in YASARA.
File extension pdb converter how to#
3 File types and how to work with them in YASARA.2.2.2 Tangent on using the command line and the interactive menus.Who owns YASARA and the other programs in this book.End of section checks and active reading.A guide to biomolecule visualization and analysis in YASARA.