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How do I move the residue label in PyMOL?
If you like to use the mouse, you can enter edit_mode and ctrl-left_click to drag labels around; ctrl-shift-left_click will let you move the labels in the z-direction.
How do you choose residues?
Use the Mouse menu to enter “Pick Atom” mode (or press “1”, the standard keyboard shortcut). Click on any protein atom and its residue will highlight, and the sequence list will scroll to display this residue. Shift-click works the same way, but adds to the current selection.
How do you select specific atoms in PyMOL?
When you left-click-and-release on an atom using the left button, PyMOL should, by default, select the entire residue: This will create an entry “(sele)” in the control panel which can be acted upon using the pop-up menus.
How do you move objects in PyMOL?
Please, select anywhere on the protein and drag through the center of the screen. Now, click near the far left-hand side of the screen and drag up. Notice the difference in rotations. By the way, in PyMOL, when you rotate objects in this way, you are actually moving the display camera around the object in space.
How does VMD choose residue?
In addition, the highlighted residue will appear in your OpenGL Display window in yellow and bond drawing method, so you can visualize it easily. Use the right button of the mouse to unselect residues. Using the shift key while pressing the mouse button allows you to pick multiple residues at the same time.
How do you select ligands in PyMOL?
Display the molecule within PyMOL and use the Preset>Pretty mode to create a ribbon diagram. Colour this by chain. At this stage you may just see the bound ligand as a tiny molecule – one bound to each polypeptide chain. Now select the Display menu at the top of the page and select the sequence option.
How do you select a specific amino acid in PyMOL?
– under “display” menu select “sequence on”. A bar will appear above the structure showing the amino acid sequence of all protein chains in the window. Use option-shift to select all aa for one chain.
How to select residues and atoms in PyMOL?
Selection of residues/atoms in Pymol – YouTube This tutorial will assists you with residue/ atoms/ chain selection commands in Pymol.Canon in D Major by Kevin MacLeod is licensed under a Creative Commons
How does the selector in Resi work in PyMOL?
The selector resi takes (+)-separated lists of identifiers, as in or, alternatively, it may take a range given with a dash The identifier for a blank field in an input file is an empty pair of quotes PyMOL> select unstruct, ss “” # A named selection is created # to contain all atoms that are not assigned # a secondary structure.
How do you calculate interface residue in pymolwiki?
First, we take the area of the complex. Then, we split the complex into two pieces, one for each chain. Next, we calculate the chain-only surface area. Lastly, we take the difference between the comeplex-based areas and the chain-only-based areas. If that value is greater than your supplied cutoff, then we call it an interface residue.
How to create a named selection in PyMOL?
PyMOL> select unstruct, ss “” # A named selection is created # to contain all atoms that are not assigned # a secondary structure. Most property selectors select matches to their identifiers