Through the detailed annotation of the cited paper or journal article in protein data bank, it has been reported that thrombin has different amino acid residues which act as active sites like Serine (ser 195th residue), Glycine( Gly 219th and 216th residue), Aspartate(Asp 189th residue), Tryptophan ( Trp 215th residue) and Tyrosine (Tyr 60th residue). We can use these GUI elements or the user can give commands to get performed actions (Figure 3).įigure 3: Screenshot of the Internal GUI buttonsĪ protein named ‘thrombin’ which forms a complex with “Napsagatran” ligand molecule, has been downloaded from the protein data bank. User can also see A,S,H,L and C labels in the two rows as different columns, these alphabets implies, Action, Show, Hide, Label and Color respectively. If there are multiple molecules, user can also select every molecule or object at same time. We can see two rows on the right side of Figure 8, labeled as ‘all’ and ‘4AX9’ where we can change individual appearance of a molecule as well as all molecules together.
User can also load the file through command line using the command load E.g., “load C: Downloads1UBQ.pdb”īy default, the loaded PDB file structure will be shown with line representation in PyMol (Figure 2).įigure 2: Screenshot of PyMol with a loaded molecule Load the downloaded PDB file into PyMol (Figure 1).įigure 1: Screenshot of standard file chooser of PyMol to load the PDB fileįile → open→ choose the PDB file where it is actually located. Middle button is used to move the molecule and the right mouse button is used to move the molecule in z axis that is to zoom in and out. The left button is used to rotate the molecule. When the molecule is loaded into PyMol the molecule can be controlled by mouse, with three buttons, left, middle (pushable ball), and right.
#PYMOL TUTORIAL HOW TO SHOW LIGAND INTERACTIONS SOFTWARE#
Installation instructions and the links to download the software or the data can be obtained through the simulator tab
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