How do you show unit cells in PyMOL?

The unit cell may be shown by using the show command. Example protein (1N6H) show in the unit cell shown with show cell.

How do I show crystal contacts in PyMOL?

PyMOL can show crystal packing information by generating the “symmetry mate”. Once a crystal structure is loaded, go to “A”, select “generate”, then “symmetry mates”. There are options to display +/- one unit cell and within xx angstrom.

How do you show axis in PyMOL?

Holding the left mouse button while the pointer is inside the molecule will cause the camera to rotate along the X and Y axes. If however the pointer is outside the molecule, the camera will rotate along the Z axis. In the PyMOL Viewing Window molecules can be viewed and directly interacted with.

How do you show proteins in PyMOL?

Click S, then cartoon to show the protein’s secondary structure in popular cartoon form. Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click H then lines.

How do you make a dimer?

Carboxylic acids form dimers by hydrogen bonding of the acidic hydrogen and the carbonyl oxygen when anhydrous. For example, acetic acid forms a dimer in the gas phase, where the monomer units are held together by hydrogen bonds. Under special conditions, most OH-containing molecules form dimers, e.g. the water dimer.

How do you identify amino acids in PyMOL?

In pymol, viewing amino acids you wish to visualize can be done easily using the following steps:

1. Load your protein structure in pymol.
2. Click on the ‘S’ button for loading the amino acid sequence sequence.
3. Find the amino acid sequence you wish to view and select them.

How do you show 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:

1. This will create an entry “(sele)” in the control panel which can be acted upon using the pop-up menus.
2. Left-clicking on the first residue should once again deselect it:

Can PyMOL predict protein structure?

The 3D structure of any protein sequence can be predicted by PyMol (http://www.pymol.org/), UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/) and Antheprot 3D (https://www.antheprot-pbil.ibcp.fr) by inputting the PDB file of the polypeptide sequence. Hope it helps!

Why is PyMOL important?

PyMOL is a cross-platform molecular graphic tool and has been widely used for 3D visualization of macromolecules. The utilities of PyMOL have been extensively enhanced by various plugins, including macromolecular analysis, homology modeling, protein–ligand docking, pharmacophore modeling, VS, and MD simulations.

What is a dimer in biology?

In biochemistry, a protein dimer is a macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers. The word dimer has roots meaning “two parts”, di- + -mer.

What is a dimer in DNA?

Pyrimidine dimers are molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions. Ultraviolet light (UV) induces the formation of covalent linkages between consecutive bases along the nucleotide chain in the vicinity of their carbon–carbon double bonds.

What is a dimer in microbiology?

Definition. noun, plural: dimers. A chemical compound composed of two identical or similar (not necessarily identical) subunits or monomers.

How do you select individual atoms in PyMOL?

Picking Atoms and Bonds

1. A single atom can be “picked” using the “Pk1” function which is CTRL/right-click.
2. Multiple atoms (up to 4) can be “picked” in series using the “PkAt” function which is CTRL/right-middle.

What can I do with PyMOL?

PyMOL is a capable molecular viewer and renderer. It can be used to prepare publication-quality figures, to share interactive results with your colleagues, or to generate pre-rendered animations. Nowadays, thousands of scientists around the world routinely rely upon PyMOL for such tasks.